From gordonp at pub.open-bio.org Wed Jul 7 12:02:48 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed Jul 7 11:44:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071602.i67G2mnT032210@pub.open-bio.org> gordonp Wed Jul 7 12:02:47 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32166/shared Modified Files: MobyPrefixResolver.java Log Message: Fixed issues with SOAP payload parsing related to namespaces and encoding schemes, works with Axis 1.1beta without warnings too moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2004/07/07 16:02:47 1.2 @@ -21,9 +21,13 @@ public class MobyPrefixResolver implements PrefixResolver{ public static final String MOBY_XML_NAMESPACE = "http://www.biomoby.org/moby"; public static final String MOBY_XML_PREFIX = "moby"; + public static final String MOBY_TRANSPORT_NAMESPACE = "http://biomoby.org/"; + public static final String MOBY_TRANSPORT_PREFIX = "mobyt"; public static final String XSI_NAMESPACE1999 = "http://www.w3.org/1999/XMLSchema-instance"; public static final String XSI_NAMESPACE2001 = "http://www.w3.org/2001/XMLSchema-instance"; public static final String XSI_PREFIX = "xsi"; + public static final String XSI1999_PREFIX = "xsi1999"; + public static final String XSI2001_PREFIX = "xsi2001"; /** * We don't really implement this as it can be extremely complicated. @@ -57,8 +61,17 @@ else if(MOBY_XML_PREFIX.equals(prefix)){ return MOBY_XML_NAMESPACE; } + else if(MOBY_TRANSPORT_PREFIX.equals(prefix)){ + return MOBY_TRANSPORT_NAMESPACE; + } else if(XSI_PREFIX.equals(prefix)){ - return XSI_NAMESPACE1999; //Crappy Perl XML Schema namespace usage is out of date + return XSI_NAMESPACE1999; //Crappy Perl XML Schema namespace usage is out of date, use it by default + } + else if(XSI1999_PREFIX.equals(prefix)){ + return XSI_NAMESPACE1999; + } + else if(XSI2001_PREFIX.equals(prefix)){ + return XSI_NAMESPACE2001; //Used by Axis } else{ return ""; // Indicates that we don't have a mapping for this prefix From gordonp at pub.open-bio.org Wed Jul 7 12:02:48 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed Jul 7 11:44:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071602.i67G2mxp032191@pub.open-bio.org> gordonp Wed Jul 7 12:02:47 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32166/client Modified Files: MobyRequest.java Log Message: Fixed issues with SOAP payload parsing related to namespaces and encoding schemes, works with Axis 1.1beta without warnings too moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/05/20 16:08:05 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/07/07 16:02:47 1.4 @@ -16,9 +16,7 @@ import javax.xml.parsers.ParserConfigurationException; import javax.xml.transform.TransformerException; import javax.xml.namespace.QName; -import org.w3c.dom.Document; -import org.w3c.dom.Node; -import org.w3c.dom.Element; +import org.w3c.dom.*; // Utilities import java.util.Hashtable; @@ -34,6 +32,7 @@ import org.w3c.dom.NodeList; import org.apache.axis.message.MessageElement; import java.io.PrintStream; +import java.io.StringBufferInputStream; /** * This class handles the WSDL transaction to request a response @@ -56,6 +55,7 @@ protected MobyDataSecondaryInstance[] secondaryData = null; protected Vector outputData = null; protected Central mobyCentral = null; + protected PrefixResolver mobyPrefixResolver = null; protected Hashtable wsdlCache = null; protected String lastWsdlCacheKey = null; @@ -69,6 +69,7 @@ protected XPathContext xpath_context; protected String responseString = null; + private XPath stringEncodedXPath; private XPath base64EncodedXPath; private XPath queryResponseXPath; private XPath simpleChildXPath; @@ -97,11 +98,20 @@ } xpath_context = new XPathContext(); - PrefixResolver mobyPrefixResolver = new MobyPrefixResolver(); + mobyPrefixResolver = new MobyPrefixResolver(); // Now compile the XPath statements that will be used fetch data from the server response try{ - base64EncodedXPath = new XPath("//*[@xsi:type=\"SOAP-ENC:base64\"]", null, mobyPrefixResolver, XPath.SELECT); + base64EncodedXPath = new XPath("//*[starts-with(substring-after(@"+ + MobyPrefixResolver.XSI1999_PREFIX+ + ":type, ':'), \"base64\") or starts-with(substring-after(@"+ + MobyPrefixResolver.XSI2001_PREFIX+ + ":type, ':'), \"base64\")]", null, mobyPrefixResolver, XPath.SELECT); + stringEncodedXPath = new XPath("//*[substring-after(@"+ + MobyPrefixResolver.XSI1999_PREFIX+ + ":type, ':')=\"string\" or substring-after(@"+ + MobyPrefixResolver.XSI2001_PREFIX+ + ":type, ':')=\"string\"]", null, mobyPrefixResolver, XPath.SELECT); queryResponseXPath = new XPath("//moby:mobyData | //mobyData", null, mobyPrefixResolver, XPath.SELECT); simpleChildXPath = new XPath("moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT); collectionChildXPath = new XPath("moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT); @@ -306,23 +316,25 @@ // Should initialize endpoint, etc. This call is AXIS SPECIFIC, otherwise you'll // have to do the call's info setting manually. //((org.apache.axis.client.Call) soapCall).setSOAPService(soapService); - soapCall.setPortTypeName(new QName("http://biomoby.org/", - mobyService.getName() + "PortType")); - soapCall.setOperationName(new QName("http://biomoby.org/", - mobyService.getName())); + soapCall.removeAllParameters(); soapCall.setTargetEndpointAddress(mobyService.getURL()); + soapCall.setPortName(new QName("http://biomoby.org/", + mobyService.getName() + "PortType")); + //soapCall.setOperationName(new QName("http://biomoby.org/", + // mobyService.getName())); soapCall.setSOAPActionURI("http://biomoby.org/#" + mobyService.getName()); - soapCall.setReturnType(XMLType.SOAP_STRING); - soapCall.removeAllParameters(); MobyData[] requiredInputData = mobyService.getPrimaryInputs(); if(requiredInputData == null) return; // A method requiring no input? else{ // There is one argument, the MOBY request object string - soapCall.addParameter("MOBYRequest", - XMLType.SOAP_STRING, - stringType, - ParameterMode.IN); + /*soapCall.setReturnType(new QName("http://biomoby.org/", mobyService.getName())); + soapCall.addParameter("MOBYRequest", + XMLType.SOAP_STRING, + stringType, + ParameterMode.IN);*/ + if(debug) + debugPS.println("Set returnType after addParameter was " + soapCall.getReturnType()); } return; } @@ -337,9 +349,12 @@ //Setup mobyXMLInputData[0] = mobyInputXML; + if(debug) + debugPS.println("returnType just before invoke call is " + soapCall.getReturnType()); Object returnedObject = null; try{ - returnedObject = soapCall.invoke(mobyXMLInputData); + returnedObject = soapCall.invoke(new QName("http://biomoby.org/", + mobyService.getName()), mobyXMLInputData); } catch(Exception e){ throw new SOAPException("While invoking SOAP Call: " + e); @@ -354,6 +369,7 @@ return decodeSOAPMessage(resultDom); //return resultDom; } catch(Exception e){ + e.printStackTrace(); throw new SOAPException("Could not get SOAP response as DOM Element: "+ e); } @@ -368,53 +384,143 @@ * @return The root element of the MOBY response DOM */ protected Element decodeSOAPMessage(Element n) throws SOAPException, MobyException{ - if(n == null){ throw new SOAPException("SOAP Message given to decode is null"); } - // Find base64 encoded elements in the SOAP message using XPath NodeList node_list = null; + Node responseNode = null; + XPath responseElementXPath = null; try{ - node_list = runXPath(base64EncodedXPath, n); + responseElementXPath = new XPath("//"+ MobyPrefixResolver.MOBY_TRANSPORT_PREFIX+ + ":"+mobyService.getName()+"Response", + null, mobyPrefixResolver, XPath.SELECT); }catch(TransformerException te){ throw new SOAPException("Cannot select SOAP nodes due to exception "+ + "while compiling XPath statement (code bug?):" +te); + } + try{ + node_list = runXPath(responseElementXPath, n); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select SOAP nodes due to exception "+ "while executing XPath statement:" +te); } if(node_list == null || node_list.getLength() == 0){ - // Note: before giving up we should really have a plain string check as per the MOBY API 0.6 - throw new SOAPException("Could not find a Base64 encoded SOAP payload"); + throw new SOAPException("Could not find a response element in SOAP payload"); } - // Do decoding for each part found - for(int i = 0; i < node_list.getLength(); i++){ - + + if(node_list.getLength() > 1){ + throw new SOAPException("Found more than one response element in SOAP payload, " + + "unable to resolve ambiguity of the payload (service provider error?)"); + } + responseNode = node_list.item(0); + + // Find base64 encoded elements in the SOAP message using XPath and + // replace them with the real decoded contents + node_list = null; + try{ + node_list = runXPath(base64EncodedXPath, responseNode); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select base64 encoded SOAP nodes due to exception "+ + "while executing XPath statement:" +te); + } + if(debug && node_list != null){ + debugPS.println("There were " + node_list.getLength() + + " base64 encoded elements in the data"); + } + + // Do decoding for each base64 part found + for(int i = 0; node_list != null && i < node_list.getLength(); i++){ org.w3c.dom.Node change = node_list.item(i); - change.normalize(); + /* Make sure the text data is all put into one contiguous piece for decoding*/ + change.normalize(); + byte[] decodedBytes = org.apache.axis.encoding.Base64.decode(change.getFirstChild().getNodeValue()); String newText = new String(decodedBytes); if(debug){ debugPS.println("New decoded text is" + newText); } - // release resources related to the Xpath execution, since we won't be using this doc anymore - releaseXPath(n); - - responseString = new String(decodedBytes); - // Parse the MOBY XML document payload - Document domDoc = null; - try{ - domDoc = docBuilder.parse(new ByteArrayInputStream(decodedBytes)); - } catch(org.xml.sax.SAXException saxe){ - throw new MobyException("The SOAP payload defining the MOBY Result " + - "could not be parsed: " + saxe); - } catch(java.io.IOException ioe){ - throw new MobyException("The SOAP payload defining the MOBY Result " + - " could not be read (from a String!)" + ioe); + // Swap out this node for the decoded data + change.getParentNode().replaceChild(n.getOwnerDocument().createTextNode(new String(decodedBytes)), + change); + } + + // Now see if there are any strings that need decoding + node_list = null; + try{ + node_list = runXPath(stringEncodedXPath, responseNode); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select base64 encoded SOAP nodes due to exception "+ + "while executing XPath statement:" +te); + } + + // Do decoding for each base64 part found + for(int i = 0; node_list != null && i < node_list.getLength(); i++){ + org.w3c.dom.Node change = node_list.item(i); + /* Make sure the text data is all put into one contiguous piece for decoding*/ + change.normalize(); + String plainString = ""; + int j = 0; + for(NodeList children = change.getChildNodes(); + children != null && j < children.getLength(); + j++){ + Node child = children.item(j); + if(child instanceof CDATASection || child instanceof Text){ + plainString += child.getNodeValue(); + } + } + + // Swap out this node for the decoded data + change.getParentNode().replaceChild(n.getOwnerDocument().createTextNode(plainString), change); + } + if(debug && node_list != null){ + debugPS.println("There were " + node_list.getLength() + + " XML Schema string encoded elements in the data"); + } + + // Parse the MOBY XML document payload + responseNode.normalize(); + NodeList children = responseNode.getChildNodes(); + if(children == null){ + throw new MobyException("The MOBY payload has no contents at all"); + } + if(children.getLength() != 1){ + debugPS.println("Warning: MOBY Payload appears to have more than " + + "just text in it, skipping the non-text sections"); + } + + responseString = ""; + for(int j = 0; j < children.getLength(); j++){ + Node child = children.item(j); + if(child instanceof CDATASection || child instanceof Text){ + responseString += child.getNodeValue(); } - return domDoc.getDocumentElement(); } - return null; //Shouldn't get here + + if(responseString.length() == 0){ + throw new MobyException("The MOBY payload has no text contents at all"); + } + + Document domDoc = null; + try{ + domDoc = docBuilder.parse(new StringBufferInputStream(responseString)); + } catch(org.xml.sax.SAXException saxe){ + throw new MobyException("The SOAP payload defining the MOBY Result " + + "could not be parsed: " + saxe); + } catch(java.io.IOException ioe){ + throw new MobyException("The SOAP payload defining the MOBY Result " + + " could not be read (from a String!)" + ioe); + } + + // release resources related to the Xpath execution, since we won't be using this doc anymore + releaseXPath(n); + + return domDoc.getDocumentElement(); } @@ -492,7 +598,7 @@ if(debug){ debugPS.println("Aha! Got " + response_list.getLength() + " mobyContent response elements"); } - // Do data deserialization for each response's mobyData + // Do data decoding for each response's mobyData for(int i = 0; i < response_list.getLength(); i++){ Node response = response_list.item(i); From gordonp at pub.open-bio.org Wed Jul 7 12:07:47 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed Jul 7 11:49:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071607.i67G7ln4032248@pub.open-bio.org> gordonp Wed Jul 7 12:07:46 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv32223 Modified Files: ChangeLog Log Message: Recorded fixes to MOBYRequest moby-live/Java/docs ChangeLog,1.15,1.16 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/05/20 16:23:15 1.15 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/07/07 16:07:46 1.16 @@ -1,3 +1,9 @@ +2004-07-07 Paul Gordon + + * Modifications to MobyRequest to handle Axis 1.1beta, and a variety of + encoding schemes (base64 and XSD string) and namespaces (1999 and 2001 + XSD, MOBY transport) + 2004-05-20 Paul Gordon * Added full working example of service discovery and invocation in From mwilkinson at pub.open-bio.org Thu Jul 8 20:21:53 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 8 20:03:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690LrIk005683@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY/Adaptor/moby Modified Files: queryapi.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/06/24 22:32:39 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/07/09 00:21:53 1.2 @@ -16,12 +16,7 @@ dbname => [undef, 'read/write'], port => [undef, 'read/write'], proxy => [undef, 'read/write'], - sourcetype => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], - url => [undef, 'read/write'], - _implementation => [undef, 'read/write'], # this is the implementation of the API, e.g. mysql - - dbh => [undef, 'read/write'], # once all the calls are converttd remove this! It should not be accessible from outside!!! - + url => [undef, 'read/write'], ); #_____________________________________________________________ @@ -41,10 +36,56 @@ } # List of names of all specified object attributes - sub _standard_keys { + sub _standard_keys_a { keys %_attr_data; } + sub username { + my ($self, $arg) = @_; + $self->{username} = $arg if defined $arg; + return $self->{username}; + } + sub password { + my ($self, $arg) = @_; + $self->{password} = $arg if defined $arg; + return $self->{password}; + } + sub dbname { + my ($self, $arg) = @_; + $self->{dbname} = $arg if defined $arg; + return $self->{dbname}; + } + sub port { + my ($self, $arg) = @_; + $self->{port} = $arg if defined $arg; + return $self->{port}; + } + sub proxy { + my ($self, $arg) = @_; + $self->{proxy} = $arg if defined $arg; + return $self->{proxy}; + } + sub sourcetype { + my ($self, $arg) = @_; + $self->{sourcetype} = $arg if defined $arg; + return $self->{sourcetype}; + } + sub url { + my ($self, $arg) = @_; + $self->{url} = $arg if defined $arg; + return $self->{url}; + } + sub _implementation { + my ($self, $arg) = @_; + $self->{'_implementation'} = $arg if defined $arg; + return $self->{'_implementation'}; + } + sub dbh { + my ($self, $arg) = @_; + $self->{dbh} = $arg if defined $arg; + return $self->{dbh}; + } + } sub new { @@ -54,7 +95,7 @@ my $self = bless {}, $class; - foreach my $attrname ( $self->_standard_keys ) { + foreach my $attrname ( $self->_standard_keys_a ) { if (exists $args{$attrname} && defined $args{$attrname}) { $self->{$attrname} = $args{$attrname} } elsif ($caller_is_obj) { @@ -62,95 +103,88 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - - my $source = $self->sourcetype; - my $datasource = $source->new(adaptor => $self); - unless ($datasource) { - print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; - return undef; - } - $self->_implementation($datasource); - - # the lines below should be removed, since this should be pushed down into the implementation - ############################################################## - unless ($datasource->dbh) { - print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; - return undef; - } - - $self->dbh($datasource->dbh); - ############################################################# - return $self; } sub insert_collection_input { - my ($self, %args) = @_; - my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ - # this should be dropped down into the mysql.pm module?? probably... - $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); - my $id=$self->dbh->{mysql_insertid}; - return $id; - } + die "insert_collection_input not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + #if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # # this should be dropped down into the mysql.pm module?? probably... + # $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + # my $id=$self->dbh->{mysql_insertid}; + # return $id; + #} } sub insert_collection_output { - my ($self, %args) = @_; - my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ - # this should be dropped down into the mysql.pm module?? probably... - $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); - my $id=$self->dbh->{mysql_insertid}; - return $id; - } + die "insert_collection_output not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + #if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # # this should be dropped down into the mysql.pm module?? probably... + # $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + # my $id=$self->dbh->{mysql_insertid}; + # return $id; + #} } sub insert_simple_input { - my ($self, %args) = @_; - my $dbh = $self->dbh; - - $dbh->do("insert into simple_input - (object_type_uri, - namespace_type_uris, - article_name, - service_instance_id, - collection_input_id) - values (?,?,?,?,?)", - undef, - ($args{object_type_uri}, - $args{namespace_type_uris}, - $args{article_name}, - $args{service_instance_id}, - $args{collection_input_id})); - my $id=$dbh->{mysql_insertid}; - return $id; + die "insert_simple_input not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + # + #$dbh->do("insert into simple_input + # (object_type_uri, + # namespace_type_uris, + # article_name, + # service_instance_id, + # collection_input_id) + # values (?,?,?,?,?)", + # undef, + # ($args{object_type_uri}, + # $args{namespace_type_uris}, + # $args{article_name}, + # $args{service_instance_id}, + # $args{collection_input_id})); + #my $id=$dbh->{mysql_insertid}; + #return $id; } sub insert_simple_output { - my ($self, %args) = @_; - my $dbh = $self->dbh; - - $dbh->do("insert into simple_output - (object_type_uri, - namespace_type_uris, - article_name, - service_instance_id, - collection_output_id) - values (?,?,?,?,?)", - undef, - ($args{object_type_uri}, - $args{namespace_type_uris}, - $args{article_name}, - $args{service_instance_id}, - $args{collection_output_id})); - my $id=$dbh->{mysql_insertid}; - return $id; + die "insert_simple_output not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + # + #$dbh->do("insert into simple_output + # (object_type_uri, + # namespace_type_uris, + # article_name, + # service_instance_id, + # collection_output_id) + # values (?,?,?,?,?)", + # undef, + # ($args{object_type_uri}, + # $args{namespace_type_uris}, + # $args{article_name}, + # $args{service_instance_id}, + # $args{collection_output_id})); + #my $id=$dbh->{mysql_insertid}; + #return $id; } +sub query_service_instance { + die "query_service_instance not implemented in adaptor\n"; +} + +sub insert_service_instance { + die "insert_service_instance not implemented in adaptor\n"; +} + sub _dump { my ($self) = @_; @@ -160,37 +194,37 @@ } sub DESTROY {} - -sub AUTOLOAD { - no strict "refs"; - my ($self, $newval) = @_; - - $AUTOLOAD =~ /.*::(\w+)/; - - my $attr=$1; - if ($self->_accessible($attr,'write')) { - - *{$AUTOLOAD} = sub { - if (defined $_[1]) { $_[0]->{$attr} = $_[1] } - return $_[0]->{$attr}; - }; ### end of created subroutine - -### this is called first time only - if (defined $newval) { - $self->{$attr} = $newval - } - return $self->{$attr}; - - } elsif ($self->_accessible($attr,'read')) { - - *{$AUTOLOAD} = sub { - return $_[0]->{$attr} }; ### end of created subroutine - return $self->{$attr} } - - - # Must have been a mistake then... - croak "No such method: $AUTOLOAD"; -} - +# +#sub AUTOLOAD { +# no strict "refs"; +# my ($self, $newval) = @_; +# +# $AUTOLOAD =~ /.*::(\w+)/; +# +# my $attr=$1; +# if ($self->_accessible($attr,'write')) { +# +# *{$AUTOLOAD} = sub { +# if (defined $_[1]) { $_[0]->{$attr} = $_[1] } +# return $_[0]->{$attr}; +# }; ### end of created subroutine +# +#### this is called first time only +# if (defined $newval) { +# $self->{$attr} = $newval +# } +# return $self->{$attr}; +# +# } elsif ($self->_accessible($attr,'read')) { +# +# *{$AUTOLOAD} = sub { +# return $_[0]->{$attr} }; ### end of created subroutine +# return $self->{$attr} } +# +# +# # Must have been a mistake then... +# croak "No such method: $AUTOLOAD"; +#} +# 1; From mwilkinson at pub.open-bio.org Thu Jul 8 20:21:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 8 20:03:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690Lshx005702@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/06/24 22:32:39 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/09 00:21:53 1.2 @@ -1,8 +1,13 @@ package MOBY::Adaptor::moby::queryapi::mysql; use strict; -use vars qw($AUTOLOAD); +use vars qw($AUTOLOAD @ISA); use Carp; +use MOBY::Adaptor::moby::queryapi; +use DBI; +use DBD::mysql; + +@ISA = qw{MOBY::Adaptor::moby::queryapi}; # implements the interface { #Encapsulated class data @@ -12,7 +17,6 @@ my %_attr_data = # DEFAULT ACCESSIBILITY ( driver => ["DBI:mysql", 'read/write'], - adaptor => [undef, 'read/write'], # I think this causes a circular reference... dbh => [undef, 'read/write'], ); @@ -38,15 +42,26 @@ keys %_attr_data; } + sub driver { + my ($self, $arg) = @_; + $self->{driver} = $arg if defined $arg; + return $self->{driver}; + } + sub dbh { + my ($self, $arg) = @_; + $self->{dbh} = $arg if defined $arg; + return $self->{dbh}; + } + } sub new { my ($caller, %args) = @_; + my $self = $caller->SUPER::new(%args); + my $caller_is_obj = ref($caller); my $class = $caller_is_obj || $caller; - my $self = bless {}, $class; - foreach my $attrname ( $self->_standard_keys ) { if (exists $args{$attrname} && defined $args{$attrname}) { $self->{$attrname} = $args{$attrname} } @@ -55,58 +70,194 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - + return unless $self->driver; - my $driver = $self->driver; - my $username = $self->adaptor->username; - my $password = $self->adaptor->password; - my $port = $self->adaptor->port; - my $url = $self->adaptor->url; - my $dbname = $self->adaptor->dbname; + my $driver = $self->driver; # inherited from the adaptorI (queryapi) + my $username = $self->username; + my $password = $self->password; + my $port = $self->port; + my $url = $self->url; + my $dbname = $self->dbname; my ($dsn) = "$driver:$dbname:$url:$port"; - #my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database"; - +# print STDERR "\n\nconnectiung to $driver:$dbname:$url:$port\n\n"; my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database"; - return undef unless $dbh; - $self->dbh($dbh); + + + ############################################################## + unless ($dbh) { + print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; + return undef; + } + + $self->dbh($dbh); + ############################################################# + + return undef unless $self->dbh; return $self; } -sub DESTROY {} +sub insert_collection_input { + my ($self, %args) = @_; + my $dbh = $self->dbh; + if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # this should be dropped down into the mysql.pm module?? probably... + $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + my $id=$self->dbh->{mysql_insertid}; + return $id; + } +} -sub AUTOLOAD { - no strict "refs"; - my ($self, $newval) = @_; - - $AUTOLOAD =~ /.*::(\w+)/; - - my $attr=$1; - if ($self->_accessible($attr,'write')) { - - *{$AUTOLOAD} = sub { - if (defined $_[1]) { $_[0]->{$attr} = $_[1] } - return $_[0]->{$attr}; - }; ### end of created subroutine - -### this is called first time only - if (defined $newval) { - $self->{$attr} = $newval +sub insert_collection_output { + my ($self, %args) = @_; + my $dbh = $self->dbh; + if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # this should be dropped down into the mysql.pm module?? probably... + $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + my $id=$self->dbh->{mysql_insertid}; + return $id; } - return $self->{$attr}; +} - } elsif ($self->_accessible($attr,'read')) { +sub insert_simple_input { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do("insert into simple_input + (object_type_uri, + namespace_type_uris, + article_name, + service_instance_id, + collection_input_id) + values (?,?,?,?,?)", + undef, + ($args{object_type_uri}, + $args{namespace_type_uris}, + $args{article_name}, + $args{service_instance_id}, + $args{collection_input_id})); + my $id=$dbh->{mysql_insertid}; + return $id; +} - *{$AUTOLOAD} = sub { - return $_[0]->{$attr} }; ### end of created subroutine - return $self->{$attr} } +sub insert_simple_output { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do("insert into simple_output + (object_type_uri, + namespace_type_uris, + article_name, + service_instance_id, + collection_output_id) + values (?,?,?,?,?)", + undef, + ($args{object_type_uri}, + $args{namespace_type_uris}, + $args{article_name}, + $args{service_instance_id}, + $args{collection_output_id})); + my $id=$dbh->{mysql_insertid}; + return $id; - # Must have been a mistake then... - croak "No such method: $AUTOLOAD"; } +sub query_service_instance { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? + q{select + service_instance_id, + category, + serviceName, + service_type_uri, + authority.authority_uri, + url, + service_instance.contact_email, + authoritative, + description + from service_instance, authority + where + service_instance.authority_id = authority.authority_id + and servicename=? and authority.authority_uri = ? + }, + undef,($args{servicename}, $args{authURI})); + return undef unless $serviceid; + return {serviceid => $serviceid, + category => $category, + name => $name, + servcetype => $typeURI, + authURI => $authURI, + url => $url, + email => $email, + authoritative => $authoritative, + desc => $desc, + }; +} + + +sub insert_service_instance { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, + undef, + $args{'category'}, + $args{'servicename'}, + $args{'service_type_uri'}, + $args{'authority_id'}, + $args{'url'}, + $args{'contact_email'}, + $args{'authoritative'}, + $args{'description'}); + + my $id = $dbh->{mysql_insertid}; + return $id; +} + + + +sub _checkURI { + +# my $uri = "http://www.ics.uci.edu/pub/ietf/uri/#Related"; +#print "$1, $2, $3, $4, $5, $6, $7, $8, $9" if +# $uri =~ m{^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?}; +# +#The license for this recipe is available here. +# +#Discussion: +# +#If the match is successful, a URL such as +# +#http://www.ics.uci.edu/pub/ietf/uri/#Related +# +#will be broken down into the following group match variables: +# +#$1 = http: +#$2 = http +#$3 = //www.ics.uci.edu +#$4 = www.ics.uci.edu +#$5 = /pub/ietf/uri/ +#$6 = +#$7 = +#$8 = #Related +#$9 = Related +# +#In general, this regular expression breaks a URI down into the following parts, +#as defined in the RFC: +# +#scheme = $2 +#authority = $4 +#path = $5 +#query = $7 +#fragment = $9 + +} + +sub DESTROY {} 1; From mwilkinson at pub.open-bio.org Thu Jul 8 20:21:53 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 8 20:03:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690LrJD005664@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY Modified Files: Central.pm Config.pm dbConfig.pm service_instance.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY Central.pm,1.131,1.132 Config.pm,1.3,1.4 dbConfig.pm,1.2,1.3 service_instance.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.131 retrieving revision 1.132 diff -u -r1.131 -r1.132 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/06/24 22:32:38 1.131 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/09 00:21:53 1.132 @@ -1942,15 +1942,16 @@ sub retrieveService { my ($pkg, $payload) = @_; + # the payload here is actually the full XML from the findService call above... #return "NOT YET IMPLEMENTED"; - my ($AuthURI, $serviceName) = &_retrieveServicePayload($payload); + my ($AuthURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML) = &_retrieveServicePayload($payload); unless ($AuthURI && $serviceName){return ""} my $SI = MOBY::service_instance->new(authority_uri => $AuthURI, servicename => $serviceName); my $wsdls; return "" unless ($SI); if ($SI->category eq 'moby'){ - my $wsdl = &_getServiceWSDL($SI); + my $wsdl = &_getServiceWSDL($SI, $InputXML, $OutputXML, $SecondaryXML); if ($wsdl){ $wsdls .= "\n"; } @@ -1976,7 +1977,27 @@ $serviceName = $x->item($n)->getAttributeNode("serviceName"); # may or may not have a name if ($serviceName){$serviceName = $serviceName->getValue()} } - return ($authURI, $serviceName); + + my $INPUT = $doc->getElementsByTagName("Input"); + my $InputXML = ""; + if ($INPUT->item(0)){ + $InputXML = $INPUT->item(0)->toString; + } + + my $OUTPUT = $doc->getElementsByTagName("Output"); + my $OutputXML = ""; + if ($OUTPUT->item(0)){ + $OutputXML = $OUTPUT->item(0)->toString; + } + + my $SECONDARY = $doc->getElementsByTagName("Output"); + my $SecondaryXML = ""; + if ($SECONDARY->item(0)){ + $SecondaryXML = $SECONDARY->item(0)->toString; + } + + return ($authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML); + } @@ -2571,7 +2592,7 @@ sub _getServiceWSDL { - my ($SI) = @_; + my ($SI, $InputXML, $OutputXML, $SecondaryXML) = @_; # the lines below causes no end of grief. It is now in a variable. #open (WSDL, "./MOBY/Central_WSDL_SandR.wsdl") || die "can't open WSDL file for search and replace\n"; #my $wsdl = join "", (); @@ -2586,8 +2607,13 @@ my $URL = $SI->url; my $IN = "NOT_YET_DEFINED_INPUTS"; my $OUT = "NOT_YET_DEFINED_OUTPUTS"; - my $INxsd = ""; - my $OUTxsd=""; + + my $INxsd = &_getInputXSD($InputXML, $SecondaryXML); + my $OUTxsd = &_getOutputXSD($OutputXML); + + $INxsd ||= ""; + $OUTxsd ||=""; + $wsdl =~ s/MOBY__SERVICE__NAME__/$serviceName/g; # replace all of the goofy portbindingpottype crap $wsdl =~ s/\<\!\-\-\s*MOBY__SERVICE__DESCRIPTION\s*\-\-\>/Authority: $AuthURI - $desc/g; # add a sensible description $wsdl =~ s/MOBY__SERVICE__URL/$URL/g; # the URL to the service @@ -3045,6 +3071,125 @@ END +=head2 _getInputXSD + + name : _getInputXSD($InputXML, $SecondaryXML) + function: to get an XSD describing the input to a MOBY Service, + e.g. to use in a WSDL document + args : (see _serviceListResponse code above for full details of XML) + $InputXML - the ... block of a findService + response message + + $SecondaryXML - the ... + fragment of a findService response message + + returns : XSD fragment of XML (should not return an XML header!) + notes : the structure of an Input block is as follows: + + + + + the structure of a secondaryArticle block is as follows: + + + + + +=over + +=item * Simple + + + ObjectOntologyTerm + NamespaceTerm + ... + + +=item * Collection note that articleName of the contained Simple objects is not required, and is ignored. + + + + ...... + ...... + + +=item * Secondary + + + + INT|FLOAT|STRING + ... + ... + ... + ... + ... + + +=back + +=cut + + +sub _getInputXSD { + my ($Input, $Secondary) =@_; + my $XSD; + + + return $XSD; +} + +=head2 _getOuputXSD + + name : _getOutputXSD($OutputXML) + function: to get an XSD describing the output from a MOBY Service + e.g. to use in a WSDL document + args : (see _serviceListResponse code above for full details) + $InputXML - the ... block of a findService + response message + + $SecondaryXML - the ... + fragment of a findService response message + + returns : XSD fragment of XML (should not return an XML header!) + notes : the structure of an Output block is as follows: + + + + +=over + +=item * Simple + + + ObjectOntologyTerm + NamespaceTerm + ... + + +=item * Collection note that articleName of the contained Simple objects is not required, and is ignored. + + + + ...... + ...... + + +=back + +=cut + +sub _getOutputXSD { + my ($Output) =@_; + my $XSD; + + + return $XSD; +} + 1; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/06/24 22:32:38 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/07/09 00:21:53 1.4 @@ -74,7 +74,7 @@ } my $file = $ENV{MOBY_CENTRAL_CONFIG}; - $file || die "can't open MOBY Configuration file $!\n"; + (-e $file) || die "can't open MOBY Configuration file $!\n"; chomp $file; if ((-e $file) && (!(-d $file))){ @@ -106,27 +106,22 @@ if ($self->{"${source}Adaptor"}){return $self->{"${source}Adaptor"}}; # read from cache - my $username = $self->$source->{username}; # $self->source returns a MOBY::dbConfig object + my $username = $self->$source->{username}; # $self->$source returns a MOBY::dbConfig object my $password = $self->$source->{password}; my $port = $self->$source->{port}; my $dbname = $self->$source->{dbname}; my $url = $self->$source->{url}; my $adaptor = $self->$source->{adaptor}; - my $sourcetype = $self->$source->{sourcetype}; eval "require $adaptor"; return undef if $@; - eval "require $sourcetype"; - return undef if $@; - my $ADAPTOR = $adaptor->new( # by default, this is queryapi - source => $source, + my $ADAPTOR = $adaptor->new( # by default, this is queryapi::mysql username => $username, password => $password, port => $port, dbname => $dbname, url => $url, - sourcetype => $sourcetype, ); if ($ADAPTOR){ $self->{"${source}Adaptor"} = $ADAPTOR; # cache it =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm 2004/06/29 16:23:59 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm 2004/07/09 00:21:53 1.3 @@ -18,8 +18,7 @@ dbname => [undef, 'read/write'], port => [undef, 'read/write'], proxy => [undef, 'read/write'], - adaptor => ["MOBY::Adaptor::moby::queryapi", 'read/write'], - sourcetype => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], + adaptor => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], url => [undef, 'read/write'], section => [undef, 'read/write'], ); @@ -44,7 +43,7 @@ sub _standard_keys { keys %_attr_data; } - # List of names of all specified object attributes + sub database_title { my ($self, $val) = @_; $self->section_title($val) if $val; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/06/24 22:32:38 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/09 00:21:53 1.6 @@ -8,6 +8,7 @@ use MOBY::central_db_connection; use MOBY::OntologyServer; use MOBY::authority; +use MOBY::Config; #@ISA = qw(MOBY::central_db_connection); # can't do this yet... @@ -74,14 +75,6 @@ description => [undef, 'read/write'], registry => ['MOBY_Central', 'read/write'], test => [0, 'read/write'], # toggles create or test_existence behaviour - - username => ["mobycentral", 'read/write'], - password => ["mobycentral", 'read/write'], - dbname => ["mobycentral", 'read/write'], - host => ["localhost", 'read/write'], - port => [3306, 'read/write'], - dbh => [undef, 'read/write'], - ); #_____________________________________________________________ @@ -147,14 +140,23 @@ (defined $val) && ($self->{description} = $val); return $self->{description} } + + sub dbh { + $CONFIG ||=MOBY::Config->new; # exported by Config.pm + my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral')->dbh; + } + sub adaptor { + $CONFIG ||=MOBY::Config->new; # exported by Config.pm + my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral'); + } } -sub _dbh { - my ($self) = @_; - - my $central_connect = MOBY::central_db_connection->new(); - $self->dbh($central_connect->dbh); -} +#sub _dbh { +# my ($self) = @_; +# +# my $central_connect = MOBY::central_db_connection->new(); +# $self->dbh($central_connect->dbh); +#} sub new { my ($caller, %args) = @_; @@ -186,13 +188,15 @@ return undef unless $self->authority_uri; return undef unless $self->servicename; - $self->_dbh(); - return undef unless $self->dbh; - my $dbh = $self->dbh; + #$self->_dbh(); + #return undef unless $self->dbh; + #my $dbh = $self->dbh; if ($self->test){ return $self->service_instance_exists} - $self->authority($self->_get_authority()); + $self->authority($self->_get_authority()); # this might not be necessary - it simply converts auth_uri to auth_id and v.v.? + # it actually is necessary for the moment. We need to put the logic of determining + # service id into the mysql.pm module!! if ($self->service_type){ my $OE = MOBY::OntologyServer->new(ontology => 'service'); @@ -201,54 +205,43 @@ ($self->service_type =~ /urn:lsid/)?$self->service_type_uri($self->service_type):$self->service_type_uri($servicetypeURI); } - my ($serviceid, $category, $name, $typeURI, $authid,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? - q{select - service_instance_id, - category, - serviceName, - service_type_uri, - authority_id, - url, - contact_email, - authoritative, - description - from service_instance where servicename=? and authority_id=?}, - undef,($self->servicename, $self->authority->authority_id)); + my $existing_service = $self->adaptor->query_service_instance (servicename => $self->servicename, authURI => $self->authority_uri); + + - if ((defined $serviceid) # if it exists, you are not allowed to have passed anything other than service name and authorityURI + if (($existing_service) # if it exists, you are not allowed to have passed anything other than service name and authorityURI && ((defined $self->category) || (defined $self->service_type) || (defined $self->url) || (defined $self->contact_email) || (defined $self->description))){ return -1; # no no no, not alowed to do that! I will not give you an object - } elsif (defined $serviceid){ # if service exists, then instantiate it from the database retrieval we just did - $self->service_instance_id($serviceid); - $self->category($category); - $self->service_type($typeURI); - $self->url($url); - $self->contact_email($email); - $self->description($desc); - $self->authority($self->_get_authority); + } elsif ($existing_service){ # if service exists, then instantiate it from the database retrieval we just did + $self->service_instance_id($existing_service->{'serviceid'}); + $self->category($existing_service->{'category'}); + $self->service_type($existing_service->{'servicetype'}); + $self->url($existing_service->{'url'}); + $self->contact_email($existing_service->{'email'}); + $self->description($existing_service->{'desc'}); + $self->authority($existing_service->{'authURI'}); $self->{__exists__} = 1; # this service already existed - } elsif (!(defined $serviceid) # if it doesn't exist + } elsif (!($existing_service) # if it doesn't exist && (defined $self->category) # and you have given me things I need to create it && (defined $self->service_type) && (defined $self->url) && (defined $self->contact_email) && (defined $self->description)) { # then create it de novo if we have enough information - $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, - undef, - $self->category, - $self->servicename, - $self->service_type_uri, - $self->authority->authority_id, - $self->url, - $self->contact_email, - $self->authoritative, - $self->description); - $self->service_instance_id($dbh->{mysql_insertid}); + my $id = $self->adaptor->insert_service_instance( + category => $self->category, + servicename => $self->servicename, + service_type_uri => $self->service_type_uri, + authority_id => $self->authority_id, + url => $self->url, + contact_email => $self->contact_email, + authoritative => $self->authoritative, + description => $self->description); + $self->service_instance_id($id); $self->{__exists__} = 1; # this service now exists } else { # if it doesn't exist, and you havne't given me anyting I need to create it, then bail out return undef; @@ -263,6 +256,8 @@ unless ($self->{__exists__}){ return undef } + $CONFIG ||=MOBY::Config->new; + $dbh->do(q{delete from service_instance where service_instance_id = ?},undef,$self->service_instance_id); $dbh->do(q{delete from simple_input where service_instance_id = ?},undef,$self->service_instance_id); $dbh->do(q{delete from simple_output where service_instance_id = ?},undef,$self->service_instance_id); @@ -299,7 +294,7 @@ } -sub _get_authority { +sub _get_authority { # there's somethign fishy here... the authority.pm object already knows about authority_id and authorty_uri, doens't it? my ($self) = @_; my $dbh = $self->dbh; my $authority; From mwilkinson at pub.open-bio.org Thu Jul 8 20:21:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 8 20:03:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690Lsns005722@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv5633/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/06/16 19:07:34 1.17 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/09 00:21:53 1.18 @@ -213,19 +213,33 @@ ["Object", ['UglyNamespace']], # Simple ]), 24, 1); +my ($si, $reg) = $C->findService( + serviceName => "myfirstservice2" +); + +$si = $si->[0]; +my $wsdl = $C->retrieveService($si); +print $wsdl; +if ($wsdl && ($wsdl =~ /\deregisterService( serviceName => "myfirstservice2", authURI => "www.illuminae.com", - ), 25, 1); + ), 26, 1); TEST($C->deregisterService( serviceName => "myfirstservice2", authURI => "www.illuminae.com", - ), 26, 0); + ), 27, 0); TEST($C->deregisterService( serviceName => "myfirstservice", authURI => "www.illuminae.com", - ), 27, 1); + ), 28, 1); TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 28, 1); TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 29, 1); From mwilkinson at pub.open-bio.org Thu Jul 8 22:44:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 8 22:26:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090244.i692imAX006132@pub.open-bio.org> mwilkinson Thu Jul 8 22:44:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory pub.open-bio.org:/tmp/cvs-serv6113 Modified Files: LocalServices.pm Log Message: added the Union and Intersection services required by the Generation Challenge Program project. The existing client will not be able to discover nor use these services. moby-live/Perl/scripts/Services LocalServices.pm,1.63,1.64 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v retrieving revision 1.63 retrieving revision 1.64 diff -u -r1.63 -r1.64 --- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2004/06/29 16:24:00 1.63 +++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2004/07/09 02:44:48 1.64 @@ -1031,6 +1031,102 @@ } +sub ObjectUnion { + my ($caller, $data) = @_; # data is raw XML + my $MOBY_RESPONSE; + my $inputs= complexServiceInputParser($data); # thos converts it to XML::DOM objects + # hashref $input->{X} = [[COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]]...] + + return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (keys %{$inputs}); + + foreach my $queryID (keys %{$inputs}){ + my @inputlist = @{$inputs->{$queryID}}; + my $input1 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + my $input2 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + # input1 is now [COLLECTION(1), [DOM1, DOM2]] + my ($type1, $DOMS1) = @{$input1}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + my ($type2, $DOMS2) = @{$input2}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + + unless (($type1 == COLLECTION) && ($type2 == COLLECTION)){ # COLLECTION is a constant exported from MOBY::CommonSubs + $MOBY_RESPONSE .= collectionResponse([], "", $queryID) ; + next; + } + + my @DOMS1 = @{$DOMS1}; + my @DOMS2 = @{$DOMS2}; + my @ALLDOMS = (@DOMS1, @DOMS2); + + my %DOMHASH; + map {$DOMHASH{"$_"} = $_} @ALLDOMS; + + foreach my $dom1(@DOMS1){ + my $ns1 = getSimpleArticleNamespaceURI($dom1); + my ($id1) = getSimpleArticleIDs([$dom1]); + foreach my $dom2(@DOMS2){ + my $ns2 = getSimpleArticleNamespaceURI($dom2); + my ($id2) = getSimpleArticleIDs([$dom2]); + + if (($ns1 eq $ns2) && ($id1 eq $id2)){ + delete $DOMHASH{"$dom2"}; + } + } + } + my @simples; + while (my ($key, $DOM) = each %DOMHASH){ + push @simples, extractRawContent($DOM); + } + $MOBY_RESPONSE .= collectionResponse(\@simples, "UnionCollection", $queryID) ; + + } + #print $MOBY_RESPONSE; +# return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter)); +} + + +sub ObjectIntersection { + my ($caller, $data) = @_; # data is raw XML + my $MOBY_RESPONSE; + my $inputs= complexServiceInputParser($data); # thos converts it to XML::DOM objects + # hashref $input->{X} = [[COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]]...] + + return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (keys %{$inputs}); + + foreach my $queryID (keys %{$inputs}){ + my @inputlist = @{$inputs->{$queryID}}; + my $input1 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + my $input2 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + # input1 is now [COLLECTION(1), [DOM1, DOM2]] + my ($type1, $DOMS1) = @{$input1}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + my ($type2, $DOMS2) = @{$input2}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + + unless (($type1 == COLLECTION) && ($type2 == COLLECTION)){ # COLLECTION is a constant exported from MOBY::CommonSubs + $MOBY_RESPONSE .= collectionResponse([], "", $queryID) ; + next; + } + + my @DOMS1 = @{$DOMS1}; + my @DOMS2 = @{$DOMS2}; + my @gooddoms; + foreach my $dom1(@DOMS1){ + my $ns1 = getSimpleArticleNamespaceURI($dom1); + my ($id1) = getSimpleArticleIDs([$dom1]); + foreach my $dom2(@DOMS2){ + my $ns2 = getSimpleArticleNamespaceURI($dom2); + my ($id2) = getSimpleArticleIDs([$dom2]); + + if (($ns1 eq $ns2) && ($id1 eq $id2)){ + push @gooddoms, extractRawContent($dom1); + } + } + } + $MOBY_RESPONSE .= collectionResponse(\@gooddoms, "IntersectionCollection", $queryID) ; + + } + print $MOBY_RESPONSE; +# return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter)); +} + + ############################################################### ###################### for My Machine Only ################### sub _dbAccess { From mwilkinson at pub.open-bio.org Sun Jul 11 20:39:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun Jul 11 20:21:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407120039.i6C0dbuC025484@pub.open-bio.org> mwilkinson Sun Jul 11 20:39:37 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv25446/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: tightening the business logic of MOBY Object registration, as I now see a few objects in the ontology that are invalid. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/09 00:21:53 1.18 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/12 00:39:37 1.19 @@ -1,13 +1,15 @@ #!/usr/bin/perl -w use MOBY::Client::Central; +my $v = 1 if ($ARGV[0] eq "verbose"); + sub TEST { # test of Registration object ($reg, $test, $expect) = @_; die "\a\a\aREG OBJECT MALFORMED" unless $reg; if ($reg->success == $expect){ - print "test $test\t\t[PASS]\n"; + print "test $test\t\t[PASS] ", ($v?($reg->message):""),"\n"; } else { - print "test $test\t\t[FAIL]\n",$reg->message,"\n\n"; + print "test $test\t\t[FAIL] ",$reg->message,"\n\n"; } } sub TEST2 { # test of ServiceInstance object listref @@ -31,8 +33,8 @@ ); -#reg first object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +#register with two ISA's -> should fail +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", contactEmail => 'your@email.address', authURI => "blah.blah.blah", @@ -42,35 +44,56 @@ ['Object', 'articleName2']], HASA => [ ['Object', 'articleName3']]} + ), '1a', 0); + +#register with no ISA's -> should fail +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", + description => "a human-readable description of the object", + contactEmail => 'your@email.address', + authURI => "blah.blah.blah", + Relationships => { + HASA => [ + ['Object', 'articleName3']]} + ), '1b', 0); + +#reg first object class with a single ISA -> should pass +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", + description => "a human-readable description of the object", + contactEmail => 'your@email.address', + authURI => "blah.blah.blah", + Relationships => { + ISA => [ + ['Object', 'articleName2']], + HASA => [ + ['Object', 'articleName3']]} ), 1, 1); #reg duplicate object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", contactEmail => 'your@email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['Object', 'article1'], - ['Object', 'articleName2']], + ['Object', 'article1'] + ], HASA => [ ['Object', 'articleName3']]} ), 2, 0); #reg second object class -TEST($C->registerObjectClass(objectType => "YetMoreCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject2", description => "a human-readable description of the object", contactEmail => 'your@email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['Object', 'article1'], ['Object', 'articleName2']], HASA => [ ['Object', 'articleName3']]} ), 3, 1); -TEST($C->registerServiceType(serviceType => "CrappyService", +TEST($C->registerServiceType(serviceType => "HypotheticalService1", description => "a human-readable description of the service", contactEmail => 'your@email.address', authURI => "blah.blah.blah", @@ -78,7 +101,7 @@ ISA => ['Retrieval','Analysis']} ), 4, 1); -TEST($C->registerServiceType(serviceType => "CrappyService", +TEST($C->registerServiceType(serviceType => "HypotheticalService1", description => "a human-readable description of the service", contactEmail => 'your@email.address', authURI => "blah.blah.blah", @@ -86,28 +109,28 @@ ISA => ['Retrieval','Analysis']} ), 5, 0); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 6, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 7, 0); -TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 8, 1); -TEST($C->deregisterServiceType(serviceType => "CrappyService"), 9, 1); -TEST($C->deregisterServiceType(serviceType => "CrappyService"), 10, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 6, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 7, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 8, 1); +TEST($C->deregisterServiceType(serviceType => "HypotheticalService1"), 9, 1); +TEST($C->deregisterServiceType(serviceType => "HypotheticalService1"), 10, 0); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your@address.here'), 11, 1); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your@address.here'), 12, 0); -TEST($C->deregisterNamespace(namespaceType =>'UglyNamespace'), 13, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 13, 1); #reg first object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", - contactEmail => 'your@email.address', + contactEmail => 'your@email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ @@ -115,19 +138,19 @@ ), 14, 1); #reg duplicate object class -TEST($C->registerObjectClass(objectType => "YetMoreCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject2", description => "a human-readable description of the object", contactEmail => 'your@email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['TotalCrap', 'article1']]} + ['HypotheticalObject1', 'article1']]} ), 15, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 16, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 16, 0); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your@address.here'), 17, 1); @@ -141,10 +164,10 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ - ['articleName1', [Object => ['UglyNamespace']]], # Simple + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], secondary => { parametername1 => { @@ -163,10 +186,10 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ - ['articleName1', [Object => ['UglyNamespace']]], # Simple + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], ), 19, 0); @@ -179,11 +202,11 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ -# ['articleName1', [[Object => ['UglyNamespace']]]], # Collection - ['articleName1', [Object => ['UglyNamespace']]], # Simple +# ['articleName1', [[Object => ['HypotheticalNamespace1']]]], # Collection + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], ), 20, 1); @@ -210,7 +233,7 @@ TEST2($C->findService( input =>[ - ["Object", ['UglyNamespace']], # Simple + ["Object", ['HypotheticalNamespace1']], # Simple ]), 24, 1); my ($si, $reg) = $C->findService( @@ -241,9 +264,9 @@ authURI => "www.illuminae.com", ), 28, 1); -TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 28, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 29, 1); -TEST($C->deregisterNamespace(namespaceType =>'UglyNamespace'), 30, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 28, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 29, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 30, 1); exit 0; From mwilkinson at pub.open-bio.org Sun Jul 11 20:39:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun Jul 11 20:21:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407120039.i6C0dbk6025465@pub.open-bio.org> mwilkinson Sun Jul 11 20:39:37 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv25446/MOBY Modified Files: Central.pm Log Message: tightening the business logic of MOBY Object registration, as I now see a few objects in the ontology that are invalid. moby-live/Perl/MOBY Central.pm,1.132,1.133 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.132 retrieving revision 1.133 diff -u -r1.132 -r1.133 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/09 00:21:53 1.132 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/12 00:39:37 1.133 @@ -260,16 +260,20 @@ return &_error("Object name may not be an URN or URI","") if $1; } + my $ISAs; # validate that the final ontology will be valid by testing against existing relationships and such while (my ($reltype, $obj) = each %{$relationships}){ my ($success, $message, $URI) = $RelOntologyServer->relationshipExists(term => $reltype, ontology => 'object'); # success = 1 if it does - $success==0 && return &_error($message, $URI ); + $success==0 && return &_error($message, $URI ); foreach (@{$obj}){ + ++$ISAs if ($URI =~ /isa$/i); my ($objectType, $articleName) = @{$_}; my ($success, $message, $URI) = $OntologyServer->objectExists(term => $objectType); # success = 1 if it does $success==0 && return &_error($message, $URI ); } } + return &_error("Object must have exactly one ISA parent in the MOBY Object ontology") unless $ISAs == 1; + $clobber = defined($clobber)?$clobber:0; $clobber = 0 unless ($clobber eq 0 || $clobber eq 1 || $clobber eq 2); # safety! my ($exists, $exists_message, $URI) = $OntologyServer->objectExists(term => $term); # success = 1 if it does From gss at pub.open-bio.org Thu Jul 15 16:18:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 15:59:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152018.i6FKI1rq011930@pub.open-bio.org> gss Thu Jul 15 16:18:01 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv11909/S-MOBY/ref-impl/core/src/org/smoby/tools Added Files: ModelRetriever.java Log Message: New class moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools ModelRetriever.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:20:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:01:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152020.i6FKKb1I012013@pub.open-bio.org> gss Thu Jul 15 16:20:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients In directory pub.open-bio.org:/tmp/cvs-serv11988/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients Modified Files: SimpleProviderEngagerPanel.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/05/27 19:37:10 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/15 20:20:37 1.2 @@ -113,11 +113,19 @@ { Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML); MOBYProvider provider = parser.parseProvider(); - String graphURI = provider.getURI(); - HTTPRequest request = HTTPRequest.newPostRequest(graphURI); - request.addParameter("graph", graphString); - HTTPResponse response = request.send(); - outputArea.setText(response.getBody()); + + if (provider == null) + { + outputArea.setText("Couldn't parse provider"); + } + else + { + String graphURI = provider.getURI(); + HTTPRequest request = HTTPRequest.newPostRequest(graphURI); + request.addParameter("graph", graphString); + HTTPResponse response = request.send(); + outputArea.setText(response.getBody()); + } } catch (UnparsableGraphException e) { From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:07:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQk3E012103@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/.settings Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:07:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkwN012085@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:07:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkOl012067@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:07:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkuH012123@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:07:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQliU012249@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlDU012205@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlHB012225@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlUT012267@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlYq012162@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlxu012184@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQk15012141@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlH1012291@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmbX012374@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlZA012314@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmBr012332@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmaL012395@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmnC012457@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQm4Q012413@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQo1w012727@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnrV012522@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmSf012480@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnJe012541@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQn4m012564@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpN3012897@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnHE012607@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoG9012649@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQm9p012354@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpEM012918@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQncw012627@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnXG012498@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQos9012668@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpSD012772@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQqtU012963@pub.open-bio.org> gss Thu Jul 15 16:26:52 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQolE012709@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmF9012436@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpAW012857@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoZp012686@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQp4d012834@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpCE012790@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnON012586@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoqc012745@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpKD012879@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQp8C012808@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQq1p012983@pub.open-bio.org> gss Thu Jul 15 16:26:52 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQqpi012939@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFCk013305@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Added Files: index.html hello-world.n3 n3.html hello-world.rdf engage.html top-frame.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello index.html,NONE,1.1 hello-world.n3,NONE,1.1 n3.html,NONE,1.1 hello-world.rdf,NONE,1.1 engage.html,NONE,1.1 top-frame.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHYE013477@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use Added Files: HTTPException.html HTTPResponse.html HTTPRequest.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use HTTPException.html,NONE,1.1 HTTPResponse.html,NONE,1.1 HTTPRequest.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGme013365@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util Added Files: RDFXMLSerialization.n3 Serialization.n3 N3Serialization.n3 index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util RDFXMLSerialization.n3,NONE,1.1 Serialization.n3,NONE,1.1 N3Serialization.n3,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREU4013154@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer Added Files: index.html search.html suggest.html dev-tools.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer index.html,NONE,1.1 search.html,NONE,1.1 suggest.html,NONE,1.1 dev-tools.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRE5o013190@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary Added Files: VocabularyDescription.html package-use.html MOBY.html package-frame.html package-tree.html package-summary.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary VocabularyDescription.html,NONE,1.1 package-use.html,NONE,1.1 MOBY.html,NONE,1.1 package-frame.html,NONE,1.1 package-tree.html,NONE,1.1 package-summary.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFmO013260@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files Added Files: index-7.html index-5.html index-12.html index-16.html index-11.html index-3.html index-1.html index-10.html index-14.html index-4.html index-9.html index-15.html index-8.html index-2.html index-6.html index-13.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files index-7.html,NONE,1.1 index-5.html,NONE,1.1 index-12.html,NONE,1.1 index-16.html,NONE,1.1 index-11.html,NONE,1.1 index-3.html,NONE,1.1 index-1.html,NONE,1.1 index-10.html,NONE,1.1 index-14.html,NONE,1.1 index-4.html,NONE,1.1 index-9.html,NONE,1.1 index-15.html,NONE,1.1 index-8.html,NONE,1.1 index-2.html,NONE,1.1 index-6.html,NONE,1.1 index-13.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREOr013137@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core Added Files: __Collection.n3 Subject.n3 Provider name oneLineDescription.n3 Subject hasMapping.n3 operatesOn Provider.n3 providerAboutURI.n3 __Collection subjectProperty.n3 __NonCollection objectProperty name.n3 subjectProperty Object.n3 keyword.n3 objectProperty.n3 __Bag operatesOn.n3 Graph __NonCollection.n3 keyword __Seq __Alt.n3 __Alt Graph.n3 oneLineDescription mapsTo.n3 __List.n3 mapsTo __Seq.n3 index.html __List providerAboutURI hasMapping __Bag.n3 Object Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core __Collection.n3,NONE,1.1 Subject.n3,NONE,1.1 Provider,NONE,1.1 name,NONE,1.1 oneLineDescription.n3,NONE,1.1 Subject,NONE,1.1 hasMapping.n3,NONE,1.1 operatesOn,NONE,1.1 Provider.n3,NONE,1.1 providerAboutURI.n3,NONE,1.1 __Collection,NONE,1.1 subjectProperty.n3,NONE,1.1 __NonCollection,NONE,1.1 objectProperty,NONE,1.1 name.n3,NONE,1.1 subjectProperty,NONE,1.1 Object.n3,NONE,1.1 keyword.n3,NONE,1.1 objectProperty.n3,NONE,1.1 __Bag,NONE,1.1 operatesOn.n3,NONE,1.1 Graph,NONE,1.1 __NonCollection.n3,NONE,1.1 keyword,NONE,1.1 __Seq,NONE,1.1 __Alt.n3,NONE,1.1 __Alt,NONE,1.1 Graph.n3,NONE,1.1 oneLineDescription,NONE,1.1 mapsTo.n3,NONE,1.1 __List.n3,NONE,1.1 mapsTo,NONE,1.1 __Seq.n3,NONE,1.1 index.html,NONE,1.1 __List,NONE,1.1 providerAboutURI,NONE,1.1 hasMapping,NONE,1.1 __Bag.n3,NONE,1.1 Object,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDBM013048@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api Added Files: deprecated-list.html overview-frame.html developer.html constant-values.html allclasses-noframe.html packages.html stylesheet.css allclasses-frame.html package-list help-doc.html serialized-form.html overview-summary.html overview-tree.html index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api deprecated-list.html,NONE,1.1 overview-frame.html,NONE,1.1 developer.html,NONE,1.1 constant-values.html,NONE,1.1 allclasses-noframe.html,NONE,1.1 packages.html,NONE,1.1 stylesheet.css,NONE,1.1 allclasses-frame.html,NONE,1.1 package-list,NONE,1.1 help-doc.html,NONE,1.1 serialized-form.html,NONE,1.1 overview-summary.html,NONE,1.1 overview-tree.html,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRD2P013064@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use Added Files: MOBYDocumentImpl.html MOBYProviderSetImpl.html MOBYDescriptorImpl.html MOBYObjectFactory.html MOBYNonNegativeIntegerConstraintImpl.html MOBYMappingElementImpl.html MOBYProviderImpl.html MOBYDateConstraintImpl.html MOBYNonPositiveIntegerConstraintImpl.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use MOBYDocumentImpl.html,NONE,1.1 MOBYProviderSetImpl.html,NONE,1.1 MOBYDescriptorImpl.html,NONE,1.1 MOBYObjectFactory.html,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.html,NONE,1.1 MOBYMappingElementImpl.html,NONE,1.1 MOBYProviderImpl.html,NONE,1.1 MOBYDateConstraintImpl.html,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:50 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREJE013172@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Added Files: .cvsignore web.xml Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDcJ013101@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use Added Files: MOBYGraph.html MOBYOntology.html MOBYSingleElement.html MOBYObject.html MOBYProviderSet.html MOBYSubject.html MOBYGraphNode.html MOBYMappingElement.html MOBYUnorderedCollection.html MOBYResource.html MOBYEnumeration.html MOBYCollection.html MOBYPropertyValueConstraint.html MOBYDocument.html MOBYLiteral.html MOBYDescriptor.html MOBYPropertyValueException.html MOBYProvider.html MOBYFixedCollection.html MOBYPropertyValue.html MOBYOrderedCollection.html MOBYResizableCollection.html MOBYPropertyValueStatement.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use MOBYGraph.html,NONE,1.1 MOBYOntology.html,NONE,1.1 MOBYSingleElement.html,NONE,1.1 MOBYObject.html,NONE,1.1 MOBYProviderSet.html,NONE,1.1 MOBYSubject.html,NONE,1.1 MOBYGraphNode.html,NONE,1.1 MOBYMappingElement.html,NONE,1.1 MOBYUnorderedCollection.html,NONE,1.1 MOBYResource.html,NONE,1.1 MOBYEnumeration.html,NONE,1.1 MOBYCollection.html,NONE,1.1 MOBYPropertyValueConstraint.html,NONE,1.1 MOBYDocument.html,NONE,1.1 MOBYLiteral.html,NONE,1.1 MOBYDescriptor.html,NONE,1.1 MOBYPropertyValueException.html,NONE,1.1 MOBYProvider.html,NONE,1.1 MOBYFixedCollection.html,NONE,1.1 MOBYPropertyValue.html,NONE,1.1 MOBYOrderedCollection.html,NONE,1.1 MOBYResizableCollection.html,NONE,1.1 MOBYPropertyValueStatement.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREjs013118@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Added Files: DiscoveryQuery.java URIInvestigator.java MissingPropertyException.java ProviderRemover.java MOBYProperties.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools DiscoveryQuery.java,NONE,1.1 URIInvestigator.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 ProviderRemover.java,NONE,1.1 MOBYProperties.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:08:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDJg013033@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph Added Files: MOBYSingleElement.html MOBYSubject.html MOBYResizableCollection.html MOBYPropertyValueException.html MOBYMappingElement.html MOBYOntology.html package-use.html MOBYPropertyValueStatement.html MOBYProviderSet.html MOBYEnumeration.html MOBYGraph.html MOBYObject.html MOBYFixedCollection.html package-tree.html MOBYOrderedCollection.html MOBYResource.html MOBYDocument.html MOBYLiteral.html MOBYUnorderedCollection.html package-summary.html package-frame.html MOBYPropertyValueConstraint.html MOBYProvider.html MOBYPropertyValue.html MOBYGraphNode.html MOBYCollection.html MOBYDescriptor.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph MOBYSingleElement.html,NONE,1.1 MOBYSubject.html,NONE,1.1 MOBYResizableCollection.html,NONE,1.1 MOBYPropertyValueException.html,NONE,1.1 MOBYMappingElement.html,NONE,1.1 MOBYOntology.html,NONE,1.1 package-use.html,NONE,1.1 MOBYPropertyValueStatement.html,NONE,1.1 MOBYProviderSet.html,NONE,1.1 MOBYEnumeration.html,NONE,1.1 MOBYGraph.html,NONE,1.1 MOBYObject.html,NONE,1.1 MOBYFixedCollection.html,NONE,1.1 package-tree.html,NONE,1.1 MOBYOrderedCollection.html,NONE,1.1 MOBYResource.html,NONE,1.1 MOBYDocument.html,NONE,1.1 MOBYLiteral.html,NONE,1.1 MOBYUnorderedCollection.html,NONE,1.1 package-summary.html,NONE,1.1 package-frame.html,NONE,1.1 MOBYPropertyValueConstraint.html,NONE,1.1 MOBYProvider.html,NONE,1.1 MOBYPropertyValue.html,NONE,1.1 MOBYGraphNode.html,NONE,1.1 MOBYCollection.html,NONE,1.1 MOBYDescriptor.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRH9l013432@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Added Files: Test.html ParserTest.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Test.html,NONE,1.1 ParserTest.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDUa013082@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl Added Files: MOBYObjectFactory.html package-use.html package-summary.html MOBYNonNegativeIntegerConstraintImpl.html MOBYDescriptorImpl.html package-frame.html MOBYNonPositiveIntegerConstraintImpl.html package-tree.html MOBYProviderImpl.html MOBYProviderSetImpl.html MOBYDocumentImpl.html MOBYMappingElementImpl.html MOBYDateConstraintImpl.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl MOBYObjectFactory.html,NONE,1.1 package-use.html,NONE,1.1 package-summary.html,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.html,NONE,1.1 MOBYDescriptorImpl.html,NONE,1.1 package-frame.html,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.html,NONE,1.1 package-tree.html,NONE,1.1 MOBYProviderImpl.html,NONE,1.1 MOBYProviderSetImpl.html,NONE,1.1 MOBYDocumentImpl.html,NONE,1.1 MOBYMappingElementImpl.html,NONE,1.1 MOBYDateConstraintImpl.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGuP013335@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test Added Files: package-frame.html Test.html package-summary.html ParserTest.html package-tree.html package-use.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test package-frame.html,NONE,1.1 Test.html,NONE,1.1 package-summary.html,NONE,1.1 ParserTest.html,NONE,1.1 package-tree.html,NONE,1.1 package-use.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREeN013226@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http Added Files: package-summary.html HTTPResponse.html package-frame.html HTTPRequest.html package-tree.html package-use.html HTTPException.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http package-summary.html,NONE,1.1 HTTPResponse.html,NONE,1.1 package-frame.html,NONE,1.1 HTTPRequest.html,NONE,1.1 package-tree.html,NONE,1.1 package-use.html,NONE,1.1 HTTPException.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFLS013290@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org Added Files: .project .classpath .mymetadata Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org .project,NONE,1.1 .classpath,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREpq013206@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot Added Files: index.html tech-overview.html log4j.properties help1.jpg help.html about.html smoby.example.properties Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot index.html,NONE,1.1 tech-overview.html,NONE,1.1 log4j.properties,NONE,1.1 help1.jpg,NONE,1.1 help.html,NONE,1.1 about.html,NONE,1.1 smoby.example.properties,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIL4013662@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Added Files: greeting greeting.n3 Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies greeting,NONE,1.1 greeting.n3,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGq5013320@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev Added Files: MOBYGraphValidationServlet.java ProviderListServlet.java OWLValidationServlet.java GraphConversionServlet.java RepositoryPrintServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev MOBYGraphValidationServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 OWLValidationServlet.java,NONE,1.1 GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGE8013380@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Added Files: HelloWorldServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGAs013410@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies Added Files: index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHe2013507@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Added Files: Util.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Util.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRG0r013350@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet Added Files: package-frame.html AbstractMobyServlet.html ParameterException.html package-summary.html package-use.html ParamReader.html package-tree.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet package-frame.html,NONE,1.1 AbstractMobyServlet.html,NONE,1.1 ParameterException.html,NONE,1.1 package-summary.html,NONE,1.1 package-use.html,NONE,1.1 ParamReader.html,NONE,1.1 package-tree.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHPx013583@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Added Files: DiscoveryServlet.java KeywordSearchServlet.java BaseServlet.java ProviderInvestigationServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets DiscoveryServlet.java,NONE,1.1 KeywordSearchServlet.java,NONE,1.1 BaseServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIvF013645@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save Added Files: index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIBQ013599@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources Added Files: inherit.gif Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources inherit.gif,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFrh013275@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter Added Files: index.html top-frame.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter index.html,NONE,1.1 top-frame.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHva013453@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser Added Files: package-use.html package-frame.html UnparsableGraphException.html Parser.html package-summary.html NonCanonicalException.html package-tree.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser package-use.html,NONE,1.1 package-frame.html,NONE,1.1 UnparsableGraphException.html,NONE,1.1 Parser.html,NONE,1.1 package-summary.html,NONE,1.1 NonCanonicalException.html,NONE,1.1 package-tree.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHEI013492@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use Added Files: MOBY.html VocabularyDescription.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use MOBY.html,NONE,1.1 VocabularyDescription.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGsb013395@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use Added Files: ParameterException.html AbstractMobyServlet.html ParamReader.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use ParameterException.html,NONE,1.1 AbstractMobyServlet.html,NONE,1.1 ParamReader.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHCQ013531@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use Added Files: NonCanonicalException.html UnparsableGraphException.html Parser.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use NonCanonicalException.html,NONE,1.1 UnparsableGraphException.html,NONE,1.1 Parser.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRH73013550@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools Added Files: client.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools client.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHV7013568@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Added Files: StorageException.java StorageManager.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageException.java,NONE,1.1 StorageManager.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIKS013624@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/.settings Added Files: org.eclipse.core.resources.prefs Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings org.eclipse.core.resources.prefs,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREX1013243@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools Added Files: package-summary.html Util.html package-tree.html package-frame.html package-use.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools package-summary.html,NONE,1.1 Util.html,NONE,1.1 package-tree.html,NONE,1.1 package-frame.html,NONE,1.1 package-use.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:28:53 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:09:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152028.i6FKSrug013743@pub.open-bio.org> gss Thu Jul 15 16:28:53 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv13718/S-MOBY/ref-impl/core/src/org/smoby/parser Modified Files: Parser.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/06/18 21:38:27 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/15 20:28:53 1.5 @@ -6,6 +6,7 @@ import org.smoby.graph.*; import org.smoby.graph.impl.*; import org.smoby.parser.*; +import org.smoby.tools.ModelRetriever; import org.smoby.tools.Util; import org.smoby.vocabulary.*; import com.hp.hpl.jena.rdf.model.*; @@ -28,17 +29,12 @@ public final static String LANGUAGE_N3 = "N3"; /** - * Inference models containing inferred statements derived using - * rdfs:subClassOf relationships. + * Since models are stored in a single Jena model, we + * segregate the single model into multiple sub-models, + * each containing an rdf:type moby:Provider statement, + * plus all statements that are reachable from it. */ - private Map inferenceModels = new HashMap(); - - /** - * Return the inference model associated with a given plain model - */ - private InfModel getInferenceModel(Model model) { - return (InfModel) inferenceModels.get(model); - } + private List subModels = new ArrayList(); /** * Create and return a parser for parsing an N3 file @@ -136,8 +132,7 @@ subModel.setNsPrefixes(model.getNsPrefixMap()); Resource subject = stmt.getSubject(); Util.addReachableStmts(model, subModel, subject, subject.getURI()); - inferenceModels.put(subModel, - ModelFactory.createRDFSModel(subModel)); + subModels.add(subModel); } } @@ -168,7 +163,7 @@ // Parse each provider // - Iterator it = inferenceModels.keySet().iterator(); + Iterator it = subModels.iterator(); while (it.hasNext()) { Model model = (Model) it.next(); @@ -374,13 +369,17 @@ /** * Return a list of statements for whom the subject is a given resource, - * whose predicates is a subproperty of moby:Property, and whose object + * whose predicate is a subproperty of moby:Property, and whose object * is a blank node. */ private List mobyPropertyStatementsOf(Resource res) { + // The statements to return + // List stmts = new ArrayList(); + // Iterate over the statements whose subjects are the resource + // StmtIterator it = res.listProperties(); while (it.hasNext()) { @@ -388,17 +387,16 @@ Property p = stmt.getPredicate(); RDFNode pval = stmt.getObject(); - Model model = res.getModel(); - Model inferenceModel = getInferenceModel(model); + // Try to retrieve a description of the property at + // its URI. + // + InfModel model = getPropertyModel(p); - if (model.contains(res, p, pval) && - inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property)) + if (isMobyProperty(p, model)) { MOBYPropertyValueStatement pvalStmt = MOBYObjectFactory.newPropertyValueStatement(stmt, model); - // See if the property - // Statement s = p.getProperty(RDFS.range); if ((s != null) && (s.getObject().canAs(Resource.class))) @@ -423,6 +421,33 @@ return stmts; } + /** + * Get the model describing a given property by doing a GET + * on its URI, and creating an inference model from it. + */ + private InfModel getPropertyModel(Property p) + { + Model model = ModelRetriever.retrieveModel(p.getURI()); + + if (model == null) { + return null; + } else { + return ModelFactory.createRDFSModel(model); + } + } + + /** + * Return whether or not the given property is a MOBY property. + * This will be true if there is a statement in the model saying + * that the property is an rdfs:subPropertyOf moby:Property. + */ + private boolean isMobyProperty(Property p, InfModel model) + { + return + model != null && + model.contains(p, RDFS.subPropertyOf, MOBY.Property); + } + private String getDataPropertyValue(Resource subject, Property property) { Statement s = subject.getModel().getProperty(subject, property); From gss at pub.open-bio.org Thu Jul 15 16:30:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:11:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUG2E013793@pub.open-bio.org> gss Thu Jul 15 16:30:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings In directory pub.open-bio.org:/tmp/cvs-serv13769/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:11:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIeY013882@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Added Files: citation-search.n3 citation-search.rdf Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citation-search.n3,NONE,1.1 citation-search.rdf,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:11:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIrT013846@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/05/27 15:31:31 1.10 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/15 20:30:18 1.11 @@ -19,7 +19,7 @@ /** * The provider description graph is stored in a file named "citationSearch" */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; + private final static String DESCRIPTION_GRAPH_FILE = "citation-search.rdf"; /** * Read the description graph from a file named "terms" in the From gss at pub.open-bio.org Thu Jul 15 16:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:11:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIjd013866@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF Modified Files: web.xml Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF web.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml 2004/06/10 23:13:44 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml 2004/07/15 20:30:18 1.3 @@ -13,7 +13,7 @@ CitationSearchServlet - /citationSearch + /citation-search From gss at pub.open-bio.org Thu Jul 15 16:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:11:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIU5013827@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings Added Files: org.eclipse.core.resources.prefs Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings org.eclipse.core.resources.prefs,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:31:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:12:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152031.i6FKV7bk013923@pub.open-bio.org> gss Thu Jul 15 16:31:07 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage In directory pub.open-bio.org:/tmp/cvs-serv13902/S-MOBY/ref-impl/queries/engage Added Files: engage-acmepubs-citation-search.rdf engage-acmepubs-citation-search.n3 Log Message: New queries moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citation-search.rdf,NONE,1.1 engage-acmepubs-citation-search.n3,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:28:04 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:18:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152028.i6FKS4n5013713@pub.open-bio.org> gss Thu Jul 15 16:28:04 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv13688/S-MOBY/ref-impl/core/src/org/smoby/vocabulary Modified Files: MOBY.java Log Message: Changed s-moby.org:8080 to semanticmoby.org moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/06/18 21:39:42 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/15 20:28:04 1.5 @@ -10,7 +10,7 @@ public static String getURI() { - return "http://www.s-moby.org:8080/terms/"; + return "http://www.semanticmoby.org/ontologies/core/"; } public static String getNsPrefix() From gss at pub.open-bio.org Thu Jul 15 16:54:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:35:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152054.i6FKsbhr014079@pub.open-bio.org> gss Thu Jul 15 16:54:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14054/S-MOBY/ref-impl/server/WebRoot Modified Files: domains.html Log Message: Minor fixes moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/06/17 17:35:52 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 20:54:37 1.5 @@ -55,7 +55,7 @@ www.acmepubs.com/citationSearch + "http://www.acmepubs.com:8080/citation-search">www.acmepubs.com/citation-search Provider description graph for acmepubs.com. Note that doing an HTTP GET on this URI @@ -83,11 +83,11 @@ www.megapubs.com/citationSearch + "http://www.megapubs.com:8080/citation-search">www.megapubs.com/citation-search Provider description graph for megapubs.com. The notes regarding the - www.acmepubs.com/citationSearch also apply to this URI.
+ www.acmepubs.com/citation-search also apply to this URI.
From gss at pub.open-bio.org Thu Jul 15 16:58:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:39:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152058.i6FKwINQ014126@pub.open-bio.org> gss Thu Jul 15 16:58:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14089/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 citation-search.n3 citation-search.rdf Log Message: Changed to be ASCII moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.7,1.8 citationSearch.n3,1.6,1.7 citation-search.n3,1.1,1.2 citation-search.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/06/16 18:50:59 1.7 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/07/15 20:58:18 1.8 @@ -1,37 +1,37 @@ - - - - - - - - - - - - - - - - - - AcmePubs Citation Search - Industry standard search - - - - - - - - - \ No newline at end of file + + + + + + + + + + + + + + + + + + AcmePubs Citation Search + Industry standard search + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/06/16 18:50:59 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/07/15 20:58:18 1.7 @@ -1,28 +1,28 @@ -@prefix acmepubs: . -@prefix acmeterms: . -@prefix pubs: . -@prefix go: . -@prefix sgd: . -@prefix moby: . -@prefix rdfs: . -@prefix rdf: . -@prefix owl: . - -acmepubs:citationSearch - a moby:Provider, pubs:citationSearch ; - moby:name "AcmePubs Citation Search" ; - moby:oneLineDescription "Industry standard search" ; - moby:operatesOn [ - a rdf:Bag ; - rdf:_1 [ - a moby:Graph ; - moby:hasMapping [ - a moby:Subject, go:GeneSymbol ; - acmeterms:geneSymbol _:bnode1 ; - moby:mapsTo [ - a moby:Object, sgd:LiteratureGuide ; - acmeterms:literatureGuideURI _:bnode2 - ] - ] - ] - ] . \ No newline at end of file +@prefix acmepubs: . +@prefix acmeterms: . +@prefix pubs: . +@prefix go: . +@prefix sgd: . +@prefix moby: . +@prefix rdfs: . +@prefix rdf: . +@prefix owl: . + +acmepubs:citationSearch + a moby:Provider, pubs:citationSearch ; + moby:name "AcmePubs Citation Search" ; + moby:oneLineDescription "Industry standard search" ; + moby:operatesOn [ + a rdf:Bag ; + rdf:_1 [ + a moby:Graph ; + moby:hasMapping [ + a moby:Subject, go:GeneSymbol ; + acmeterms:geneSymbol _:bnode1 ; + moby:mapsTo [ + a moby:Object, sgd:LiteratureGuide ; + acmeterms:literatureGuideURI _:bnode2 + ] + ] + ] + ] . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3 2004/07/15 20:30:18 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3 2004/07/15 20:58:18 1.2 @@ -1,28 +1,28 @@ -@prefix acmepubs: . -@prefix acmeterms: . -@prefix pubs: . -@prefix go: . -@prefix sgd: . -@prefix moby: . -@prefix rdfs: . -@prefix rdf: . -@prefix owl: . - -acmepubs:citation-search - a moby:Provider, pubs:citationSearch ; - moby:name "AcmePubs Citation Search" ; - moby:oneLineDescription "Industry standard search" ; - moby:operatesOn [ - a rdf:Bag ; - rdf:_1 [ - a moby:Graph ; - moby:hasMapping [ - a moby:Subject, go:GeneSymbol ; - acmeterms:geneSymbol _:bnode1 ; - moby:mapsTo [ - a moby:Object, sgd:LiteratureGuide ; - acmeterms:literatureGuideURI _:bnode2 - ] - ] - ] +@prefix acmepubs: . +@prefix acmeterms: . +@prefix pubs: . +@prefix go: . +@prefix sgd: . +@prefix moby: . +@prefix rdfs: . +@prefix rdf: . +@prefix owl: . + +acmepubs:citation-search + a moby:Provider, pubs:citationSearch ; + moby:name "AcmePubs Citation Search" ; + moby:oneLineDescription "Industry standard search" ; + moby:operatesOn [ + a rdf:Bag ; + rdf:_1 [ + a moby:Graph ; + moby:hasMapping [ + a moby:Subject, go:GeneSymbol ; + acmeterms:geneSymbol _:bnode1 ; + moby:mapsTo [ + a moby:Object, sgd:LiteratureGuide ; + acmeterms:literatureGuideURI _:bnode2 + ] + ] + ] ] . \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf 2004/07/15 20:30:18 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf 2004/07/15 20:58:18 1.2 @@ -1,37 +1,37 @@ - - - - - - - - - - - - - Industry standard search - - AcmePubs Citation Search - - - - - - - - - - - - + + + + + + + + + + + + + Industry standard search + + AcmePubs Citation Search + + + + + + + + + + + + \ No newline at end of file From gss at pub.open-bio.org Thu Jul 15 17:01:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:42:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1II3014182@pub.open-bio.org> gss Thu Jul 15 17:01:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14159/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Removed Files: citationSearch.rdf citationSearch.n3 Log Message: Changed name to citation-search moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.8,NONE citationSearch.n3,1.7,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/citationSearch.rdf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/citationSearch.n3,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 17:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:42:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1gtu014225@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms Modified Files: literatureGuideURI.n3 literatureGuideURI geneSymbol geneSymbol.n3 Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms literatureGuideURI.n3,1.1,1.2 literatureGuideURI,1.1,1.2 geneSymbol,1.1,1.2 geneSymbol.n3,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . -@prefix moby: . +@prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain sgd:LiteratureGuide ; - rdfs:range xsd:anyURI . \ No newline at end of file + rdfs:range xsd:anyURI . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - \ No newline at end of file + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . -@prefix moby: . +@prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain go:GeneSymbol ; - rdfs:range xsd:string . \ No newline at end of file + rdfs:range xsd:string . From gss at pub.open-bio.org Thu Jul 15 17:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:42:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1gjA014257@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms Modified Files: literatureGuideURI.n3 geneSymbol geneSymbol.n3 literatureGuideURI Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms literatureGuideURI.n3,1.1,1.2 geneSymbol,1.1,1.2 geneSymbol.n3,1.1,1.2 literatureGuideURI,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . -@prefix moby: . +@prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain sgd:LiteratureGuide ; - rdfs:range xsd:anyURI . \ No newline at end of file + rdfs:range xsd:anyURI . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - \ No newline at end of file + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . -@prefix moby: . +@prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain go:GeneSymbol ; - rdfs:range xsd:string . \ No newline at end of file + rdfs:range xsd:string . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + From gss at pub.open-bio.org Thu Jul 15 17:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:42:50 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1goc014280@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.6,1.7 citationSearch.rdf,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/06/16 18:51:13 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/07/15 21:01:42 1.7 @@ -3,7 +3,7 @@ @prefix pubs: . @prefix go: . @prefix sgd: . -@prefix moby: . +@prefix moby: . @prefix rdfs: . @prefix rdf: . @prefix owl: . @@ -25,4 +25,4 @@ ] ] ] - ] . \ No newline at end of file + ] . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/06/16 18:51:13 1.7 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/07/15 21:01:42 1.8 @@ -6,16 +6,16 @@ xmlns:go="http://www.go.org:8080/terms/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms/" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:megaterms="http://www.megapubs.com:8080/terms/" > - + - + Cool new search @@ -27,11 +27,11 @@ - + - + From gss at pub.open-bio.org Thu Jul 15 17:02:11 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:43:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2BQ7014323@pub.open-bio.org> gss Thu Jul 15 17:02:11 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14298/S-MOBY/ref-impl/server/WebRoot Modified Files: domains.html Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 20:54:37 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 21:02:11 1.6 @@ -83,7 +83,7 @@ www.megapubs.com/citation-search + "http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch Provider description graph for megapubs.com. The notes regarding the From gss at pub.open-bio.org Thu Jul 15 17:02:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:43:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2dPj014357@pub.open-bio.org> gss Thu Jul 15 17:02:39 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage In directory pub.open-bio.org:/tmp/cvs-serv14328/S-MOBY/ref-impl/queries/engage Modified Files: engage-acmepubs-citationSearch.rdf engage-acmepubs-citationSearch.n3 Log Message: Minor changes moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.rdf,1.2,1.3 engage-acmepubs-citationSearch.n3,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf 2004/06/10 23:27:41 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf 2004/07/15 21:02:39 1.3 @@ -6,35 +6,35 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:pubs="http://www.pubs.org:8081/terms#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - + REV7 - + - + - + - + @@ -48,18 +48,18 @@ Industry standard search http://www.acmepubs.com/about/citationSearch - + AcmePubs Citation Search REV5 - + - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3 2004/06/10 23:27:12 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3 2004/07/15 21:02:39 1.3 @@ -3,7 +3,7 @@ @prefix acmepubs: . @prefix go: . @prefix sgd: . -@prefix moby: . +@prefix moby: . @prefix rdfs: . @prefix rdf: . @prefix owl: . From gss at pub.open-bio.org Thu Jul 15 17:02:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 15 16:43:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2doH014380@pub.open-bio.org> gss Thu Jul 15 17:02:39 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery In directory pub.open-bio.org:/tmp/cvs-serv14328/S-MOBY/ref-impl/queries/discovery Modified Files: query.rdf query.n3 Log Message: Minor changes moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.3,1.4 query.n3,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf 2004/06/18 21:45:07 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf 2004/07/15 21:02:39 1.4 @@ -2,17 +2,17 @@ xmlns:sgd="http://www.sgd.org:8080/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:go="http://www.go.org:8080/terms/" - xmlns:moby="http://www.s-moby.org:8080/terms/" > + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" > - + - + - + @@ -22,6 +22,6 @@ - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3 2004/06/18 21:45:07 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3 2004/07/15 21:02:39 1.4 @@ -1,6 +1,6 @@ @prefix go: . @prefix sgd: . -@prefix moby: . +@prefix moby: . @prefix rdf: . _:provider From gss at pub.open-bio.org Mon Jul 19 14:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Jul 19 14:02:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILat5004196@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/graph Modified Files: MOBYDescriptor.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYDescriptor.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/19 18:21:36 1.2 @@ -2,6 +2,8 @@ import java.net.URI; +import com.hp.hpl.jena.rdf.model.Resource; + /** * The Resource interface represents things that are available * at a URI. @@ -11,5 +13,5 @@ /** * Return the URI represented by this node. */ - public String getURI(); + public Resource getResource(); } From gss at pub.open-bio.org Mon Jul 19 14:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Jul 19 14:02:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILaer004215@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/parser Modified Files: Parser.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/15 20:28:53 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/19 18:21:36 1.6 @@ -212,8 +212,8 @@ // oneLineDescription, aboutURI, and collection of operatesOn subgraphs // return MOBYObjectFactory.newProvider( - provider.getURI(), name, oneLiner, aboutURI, - MOBYObjectFactory.newUnorderedCollection(null, operatesOn, model), + provider, name, oneLiner, aboutURI, + MOBYObjectFactory.newUnorderedCollection(provider, operatesOn, model), model); } @@ -234,7 +234,7 @@ // hasMapping property that leads to its mapping subgraph. // Resource hasMapping = getResourcePropertyValue(res, MOBY.hasMapping); - return MOBYObjectFactory.newGraph(null, parseHasMapping(hasMapping), model); + return MOBYObjectFactory.newGraph(res, parseHasMapping(hasMapping), model); } else { @@ -318,9 +318,9 @@ // Create and return a Subject to describe this hasMapping subgraph // - return MOBYObjectFactory.newSubject(res.getURI(), - MOBYObjectFactory.newFixedCollection(null, statements, model), - MOBYObjectFactory.newUnorderedCollection(null, directMappings, model), + return MOBYObjectFactory.newSubject(res, + MOBYObjectFactory.newFixedCollection(res, statements, model), + MOBYObjectFactory.newUnorderedCollection(res, directMappings, model), collectionFor(res, nestedMappings), model); } @@ -362,8 +362,8 @@ // Create and return a new MOBYObject // Model model = res.getModel(); - return MOBYObjectFactory.newObject(res.getURI(), - MOBYObjectFactory.newFixedCollection(null, statements, model), + return MOBYObjectFactory.newObject(res, + MOBYObjectFactory.newFixedCollection(res, statements, model), collectionFor(res, nested), model); } @@ -486,13 +486,13 @@ private MOBYCollection collectionFor(Resource res, List elements) { if (isList(res)) { - return MOBYObjectFactory.newFixedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newFixedCollection(res, elements, res.getModel()); } else if (isBag(res)) { - return MOBYObjectFactory.newUnorderedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newUnorderedCollection(res, elements, res.getModel()); } else if (isSeq(res)) { - return MOBYObjectFactory.newOrderedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newOrderedCollection(res, elements, res.getModel()); } else if (isAlt(res)) { - return MOBYObjectFactory.newEnumeration(null, elements, res.getModel()); + return MOBYObjectFactory.newEnumeration(res, elements, res.getModel()); } else { return null; } From gss at pub.open-bio.org Mon Jul 19 14:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Jul 19 14:02:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILaxW004177@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/graph/impl Modified Files: MOBYProviderImpl.java MOBYFixedCollectionImpl.java MOBYResizableCollectionImpl.java MOBYObjectImpl.java MOBYUnorderedCollectionImpl.java MOBYDocumentImpl.java MOBYGraphImpl.java MOBYMappingElementImpl.java MOBYOrderedCollectionImpl.java MOBYOntologyImpl.java MOBYEnumerationImpl.java MOBYDescriptorImpl.java MOBYCollectionImpl.java MOBYSubjectImpl.java MOBYGraphNodeImpl.java MOBYSingleElementImpl.java MOBYObjectFactory.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderImpl.java,1.1,1.2 MOBYFixedCollectionImpl.java,1.1,1.2 MOBYResizableCollectionImpl.java,1.1,1.2 MOBYObjectImpl.java,1.1,1.2 MOBYUnorderedCollectionImpl.java,1.1,1.2 MOBYDocumentImpl.java,1.1,1.2 MOBYGraphImpl.java,1.1,1.2 MOBYMappingElementImpl.java,1.1,1.2 MOBYOrderedCollectionImpl.java,1.1,1.2 MOBYOntologyImpl.java,1.1,1.2 MOBYEnumerationImpl.java,1.1,1.2 MOBYDescriptorImpl.java,1.1,1.2 MOBYCollectionImpl.java,1.1,1.2 MOBYSubjectImpl.java,1.1,1.2 MOBYGraphNodeImpl.java,1.1,1.2 MOBYSingleElementImpl.java,1.1,1.2 MOBYObjectFactory.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java 2004/07/19 18:21:36 1.2 @@ -16,11 +16,11 @@ private MOBYUnorderedCollection operatesOn; private Model underlying; - MOBYProviderImpl(String uri, String name, String oneLineDescription, + MOBYProviderImpl(Resource resource, String name, String oneLineDescription, String moreInfoURI, MOBYUnorderedCollection operatesOn, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.name = name; this.oneLineDescription = oneLineDescription; this.moreInfoURI = moreInfoURI; =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,16 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYFixedCollectionImpl extends MOBYCollectionImpl implements MOBYFixedCollection { - public MOBYFixedCollectionImpl(String uri, List elements, Model underlying) + public MOBYFixedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isResizable() { return false; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,16 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; abstract class MOBYResizableCollectionImpl extends MOBYCollectionImpl implements MOBYResizableCollection { - MOBYResizableCollectionImpl(String uri, List elements, Model underlying) + MOBYResizableCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isResizable() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java 2004/07/19 18:21:36 1.2 @@ -3,14 +3,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYObjectImpl extends MOBYMappingElementImpl implements MOBYObject { - MOBYObjectImpl(String uri, MOBYFixedCollection statements, + MOBYObjectImpl(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedElements, Model underlying) { - super(uri, statements, nestedElements, underlying); + super(resource, statements, nestedElements, underlying); } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,14 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYUnorderedCollectionImpl extends MOBYResizableCollectionImpl implements MOBYUnorderedCollection { - MOBYUnorderedCollectionImpl(String uri, List elements, Model underlying) + MOBYUnorderedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isOrdered() { return false; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java 2004/07/19 18:21:36 1.2 @@ -8,8 +8,8 @@ extends MOBYDescriptorImpl implements MOBYDocument { - MOBYDocumentImpl(String uri, Model underlying) + MOBYDocumentImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYGraphImpl extends MOBYSingleElementImpl @@ -10,9 +11,9 @@ { private MOBYGraphNode hasMapping; - MOBYGraphImpl(String uri, MOBYGraphNode hasMapping, Model underlying) + MOBYGraphImpl(Resource resource, MOBYGraphNode hasMapping, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.hasMapping = hasMapping; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; public class MOBYMappingElementImpl extends MOBYSingleElementImpl @@ -11,10 +12,10 @@ private MOBYFixedCollection statements; private MOBYCollection nestedElements; - public MOBYMappingElementImpl(String uri, MOBYFixedCollection statements, + public MOBYMappingElementImpl(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedElements, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.statements = statements; this.nestedElements = nestedElements; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYOrderedCollectionImpl extends MOBYResizableCollectionImpl implements MOBYOrderedCollection { - - public MOBYOrderedCollectionImpl(String uri, List elements, Model underlying) + public MOBYOrderedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isOrdered() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java 2004/07/19 18:21:36 1.2 @@ -7,7 +7,7 @@ extends MOBYDocumentImpl implements MOBYOntology { - MOBYOntologyImpl(String uri, Model underlying) { - super(uri, underlying); + MOBYOntologyImpl(Resource resource, Model underlying) { + super(resource, underlying); } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java 2004/07/19 18:21:36 1.2 @@ -10,9 +10,9 @@ extends MOBYUnorderedCollectionImpl implements MOBYEnumeration { - MOBYEnumerationImpl(String uri, List elements, Model underlying) + MOBYEnumerationImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isEnumeration() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java 2004/07/19 18:21:36 1.2 @@ -6,21 +6,26 @@ public abstract class MOBYDescriptorImpl implements MOBYDescriptor { protected Model underlying; - protected String uri; + protected Resource resource; - MOBYDescriptorImpl(String uri, Model underlying) + MOBYDescriptorImpl(Resource resource, Model underlying) { - this.uri = uri; + this.resource = resource; this.underlying = underlying; } - public String getURI() + public Resource getResource() { - return uri; + return resource; } public Model getUnderlying() { return underlying; } + + public String getURI() + { + return (resource == null) ? null : resource.getURI(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -1,9 +1,7 @@ package org.smoby.graph.impl; import org.smoby.graph.*; - -import com.hp.hpl.jena.rdf.model.Model; - +import com.hp.hpl.jena.rdf.model.*; import java.util.*; abstract class MOBYCollectionImpl @@ -12,9 +10,9 @@ { protected List elements = new ArrayList(); - MOBYCollectionImpl(String uri, List elements, Model underlying) + MOBYCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, underlying); + super(resource, underlying); for (Iterator it = elements.iterator(); it.hasNext();) { this.elements.add(it.next()); } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYSubjectImpl extends MOBYMappingElementImpl @@ -10,11 +11,11 @@ { private MOBYUnorderedCollection directMappings; - MOBYSubjectImpl(String uri, MOBYFixedCollection statements, + MOBYSubjectImpl(Resource resource, MOBYFixedCollection statements, MOBYUnorderedCollection directMappings, MOBYCollection nestedMappings, Model underlying) { - super(uri, statements, nestedMappings, underlying); + super(resource, statements, nestedMappings, underlying); this.directMappings = directMappings; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java 2004/07/19 18:21:36 1.2 @@ -1,19 +1,18 @@ package org.smoby.graph.impl; import org.smoby.graph.*; - -import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.*; abstract class MOBYGraphNodeImpl extends MOBYDescriptorImpl implements MOBYGraphNode { - MOBYGraphNodeImpl(String uri, Model underlying) + MOBYGraphNodeImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } public boolean isBlank() { - return getURI() == null; + return (resource == null) || (resource.getURI() == null); } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java 2004/07/19 18:21:36 1.2 @@ -5,14 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYSingleElementImpl extends MOBYGraphNodeImpl implements MOBYSingleElement { - MOBYSingleElementImpl(String uri, Model underlying) + MOBYSingleElementImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } public boolean isSingular() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java 2004/06/18 21:37:52 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java 2004/07/19 18:21:36 1.3 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import org.smoby.graph.impl.*; import com.hp.hpl.jena.rdf.model.*; + import java.util.*; /** @@ -11,32 +12,32 @@ */ public final class MOBYObjectFactory { - public static MOBYFixedCollection newFixedCollection(String uri, List elements, Model underlying) + public static MOBYFixedCollection newFixedCollection(Resource resource, List elements, Model underlying) { - return new MOBYFixedCollectionImpl(uri, elements, underlying); + return new MOBYFixedCollectionImpl(resource, elements, underlying); } - public static MOBYOrderedCollection newOrderedCollection(String uri, List elements, Model underlying) + public static MOBYOrderedCollection newOrderedCollection(Resource resource, List elements, Model underlying) { - return new MOBYOrderedCollectionImpl(uri, elements, underlying); + return new MOBYOrderedCollectionImpl(resource, elements, underlying); } - public static MOBYUnorderedCollection newUnorderedCollection(String uri, List elements, Model underlying) + public static MOBYUnorderedCollection newUnorderedCollection(Resource resource, List elements, Model underlying) { - return new MOBYUnorderedCollectionImpl(uri, elements, underlying); + return new MOBYUnorderedCollectionImpl(resource, elements, underlying); } - public static MOBYEnumeration newEnumeration(String uri, List elements, Model underlying) + public static MOBYEnumeration newEnumeration(Resource resource, List elements, Model underlying) { - return new MOBYEnumerationImpl(uri, elements, underlying); + return new MOBYEnumerationImpl(resource, elements, underlying); } public static MOBYProvider newProvider( - String uri, String name, String oneLineDescription, + Resource resource, String name, String oneLineDescription, String moreInfoURI, MOBYUnorderedCollection operatesOn, Model underlying) { - return new MOBYProviderImpl(uri, name, oneLineDescription, moreInfoURI, operatesOn, + return new MOBYProviderImpl(resource, name, oneLineDescription, moreInfoURI, operatesOn, underlying); } @@ -45,24 +46,24 @@ return new MOBYProviderSetImpl(); } - public static MOBYGraph newGraph(String uri, MOBYGraphNode hasMapping, Model underlying) + public static MOBYGraph newGraph(Resource resource, MOBYGraphNode hasMapping, Model underlying) { - return new MOBYGraphImpl(uri, hasMapping, underlying); + return new MOBYGraphImpl(resource, hasMapping, underlying); } public static MOBYSubject newSubject( - String uri, MOBYFixedCollection statements, + Resource resource, MOBYFixedCollection statements, MOBYUnorderedCollection directMappings, MOBYCollection nestedMappings, Model underlying) { - return new MOBYSubjectImpl(uri, statements, directMappings, + return new MOBYSubjectImpl(resource, statements, directMappings, nestedMappings, underlying); } - public static MOBYObject newObject(String uri, MOBYFixedCollection statements, + public static MOBYObject newObject(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedMappings, Model underlying) { - return new MOBYObjectImpl(uri, statements, nestedMappings, underlying); + return new MOBYObjectImpl(resource, statements, nestedMappings, underlying); } public static MOBYPropertyValueStatement newPropertyValueStatement( From gss at pub.open-bio.org Mon Jul 19 17:22:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Jul 19 17:02:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407192122.i6JLM94E004903@pub.open-bio.org> gss Mon Jul 19 17:22:09 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv4878/src/org/smoby/vocabulary Modified Files: MOBY.java Log Message: Added keyword property moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/15 20:28:04 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/19 21:22:09 1.6 @@ -36,4 +36,5 @@ public static final Property mapsTo = property(getURI(), "mapsTo"); public static final Property lastModifiedDate = property(getURI(), "lastModifiedDate"); public static final Property Property = property(getURI(), "Property"); + public static final Property keyword = property(getURI(), "keyword"); } \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 17:59:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:40:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212159.i6LLxocL012810@pub.open-bio.org> gss Wed Jul 21 17:59:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv12789/S-MOBY/ref-impl/core/src/org/smoby/graph Added Files: MOBYGraphVisitor.java Log Message: Placeholder moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYGraphVisitor.java,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 18:00:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:40:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212200.i6LM0KnH012853@pub.open-bio.org> gss Wed Jul 21 18:00:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv12828/S-MOBY/ref-impl/semanticmoby.org Modified Files: .mymetadata Log Message: Minor changes moby-live/S-MOBY/ref-impl/semanticmoby.org .mymetadata,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata 2004/07/21 22:00:20 1.2 @@ -1,6 +1,7 @@ - + From gss at pub.open-bio.org Wed Jul 21 18:01:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1GA7012884@pub.open-bio.org> gss Wed Jul 21 18:01:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv12860/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Jul 21 18:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JRA012926@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Added Files: cshl-logo.jpg nsf-logo.jpg help1.png ncgr-logo.jpg rdf-logo.PNG Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images cshl-logo.jpg,NONE,1.1 nsf-logo.jpg,NONE,1.1 help1.png,NONE,1.1 ncgr-logo.jpg,NONE,1.1 rdf-logo.PNG,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 18:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JKj012949@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Modified Files: KeywordSearchServlet.java BaseServlet.java Added Files: ProviderEngagementServlet.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets ProviderEngagementServlet.java,NONE,1.1 KeywordSearchServlet.java,1.1,1.2 BaseServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:01:19 1.2 @@ -1,10 +1,11 @@ package org.smoby.ref.servlets; import java.io.*; - +import java.util.*; import javax.servlet.*; import javax.servlet.http.*; -import javax.servlet.http.HttpServletResponse; +import org.smoby.graph.*; +import org.smoby.ref.tools.*; public class KeywordSearchServlet extends BaseServlet { @@ -12,37 +13,121 @@ throws ServletException, IOException { PrintStream out = new PrintStream(response.getOutputStream()); + + List provider = getKeywords("provider", request); + List accepts = getKeywords("accepts", request); + List returns = getKeywords("returns", request); + startHTML(response, out); + if ((provider == null) && (accepts == null) && (returns == null)) + { + showResultCount(-1, out); + } + else + { + KeywordQuery q = new KeywordQuery(provider, accepts, returns); + + List matching = q.findMatchingProviders(); + + showResultCount(matching.size(), out); + + for (Iterator it = matching.iterator(); it.hasNext();) + { + MOBYProvider p = (MOBYProvider) it.next(); + showProvider(p, out); + } + } finishHTML(response, out); } - private void startHTML(HttpServletResponse response, PrintStream out) + private List getKeywords(String paramName, HttpServletRequest request) { - response.setContentType("text/html"); - out.println(""); - out.println(""); - out.println("Semantic MOBY search results"); - out.println(""); - out.println("

"); - out.println("Semantic"); - out.println("M" + - "OBY"); - out.println("

"); + List keywords = new ArrayList(); + + String value = request.getParameter(paramName); + if (value == null) return keywords; + + value = value.trim(); + + if (value.length() == 0) return keywords; + + StreamTokenizer st = new StreamTokenizer(new StringReader(value)); + st.wordChars('*', '*'); + st.wordChars('%', '%'); + try + { + while (st.nextToken() != StreamTokenizer.TT_EOF) + { + if (st.sval != null) + { + String val = st.sval.toLowerCase().trim().replace('*', '%'); + keywords.add(val); + } + } + } catch (IOException e) {} + + return keywords; } private void showResultCount(int count, PrintStream out) { - if (count < 1) { - out.println("No matches"); + out.println(""); + out.println(""); + out.println(""); + out.println(""); + out.println("
"); + + if (count < 0) { + out.println("No keywords were entered, so no search was performed."); + } else if (count < 1) { + out.println("No matching providers were found. Note that"); + out.println("very few providers have yet been defined."); } else { - out.println("" + count + " results found:"); + out.println(count + " matching provider" + + (count > 1 ? "s" : "") + " found"); } + out.println("
"); + out.println("
"); } - private void finishHTML(HttpServletResponse response, PrintStream out) + private void showProvider(MOBYProvider provider, PrintStream out) { - response.setContentType("text/html"); - out.println(""); + String uri = provider.getResource().getURI(); + String name = provider.getName(); + String description = provider.getOneLineDescription(); + String moreInfo = provider.getMoreInfoURI(); + + out.println(""); + out.print(""); + if ((name != null) && (name.trim().length() > 0)) { + out.println(name); + } else { + out.println(uri); + } + out.print(""); + out.println(""); + out.print(""); + out.print("\"Definition\""); + out.print(""); + out.println("
"); + + if ((description != null) && (description.trim().length() > 0)) { + out.println(description); + } else { + out.println("No description is available for this provider."); + } + out.println("
"); + + if ((moreInfo != null) && (moreInfo.trim().length() > 0)) { + out.println("For more information see " + moreInfo + ""); + } + out.println("
"); } public void doPost(HttpServletRequest request, HttpServletResponse response) =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java 2004/07/21 22:01:19 1.2 @@ -5,6 +5,7 @@ import javax.servlet.*; import javax.servlet.http.*; + import org.smoby.ref.tools.*; import org.smoby.servlet.*; import org.apache.log4j.*; @@ -48,4 +49,32 @@ } } } + + protected void startHTML(HttpServletResponse response, PrintStream out) + { + response.setContentType("text/html"); + out.println(""); + out.println(""); + out.println("Semantic MOBY search results"); + out.println(""); + out.println("
"); + out.println("

"); + out.println(""); + out.println("Semantic"); + out.println("M" + + "OBY" + + ""); + out.println(""); + out.println("

"); + out.println("
"); + out.println(""); + out.println(""); + } + + protected void finishHTML(HttpServletResponse response, PrintStream out) + { + out.println(""); + out.println(""); + out.println(""); + } } \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 18:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JDv012969@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Modified Files: HelloWorldServlet.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/15 20:27:16 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/21 22:01:19 1.2 @@ -4,6 +4,7 @@ import java.util.*; import javax.servlet.*; import javax.servlet.http.*; + import org.smoby.graph.*; import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.ref.servlets.*; @@ -48,4 +49,12 @@ // Silently ignore graphs without the required form catch (Throwable t) {} } + + /** + * Return the last modification date of the description graph file + */ + public long getLastModified(HttpServletRequest request) + { + return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); + } } From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KvG013015@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot Modified Files: help.html index.html Added Files: .cvsignore Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot .cvsignore,NONE,1.1 help.html,1.1,1.2 index.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:01:20 1.2 @@ -1,26 +1,56 @@ -Semantic MOBY Help +Semantic MOBY Search Help

Semantic MOBY -Help +Search Help

-
-

+ Semantic MOBY maintains a searchable repository of descriptions of -providers of services that are available on the web. At the heart -of these descriptions is the notion of mapping, that a provider -"accepts" one type of thing, maps it to another thing that it returns -as a result. For example, entering -the following terms is asking Semantic MOBY to search its repository -for providers that accept terms described as "gene symbols" and return -things whose descriptions match the wildcard pattern "publication*". +providers of services that are available on the web. At the heart +of these descriptions is the notion that providers map one type +of thing (what the provider accepts) to another type of thing (what +the provider returns). +

+Providers, as well as things accepted and returned by providers, are +classified using web-accessible descriptions, and these descriptions +have keywords associated with them. For example, the following shows +a query for providers whose descriptions include the keyword "hello":

-. +.
+
+Search hints +
    +
  • Keywords are not case sensitive, so HELLO means the +same thing as hello as does HeLloW. +

    +
  • The wildcard character (*) can be used at the end of a keyword +to match keywords that start with the characters before the wildcard. +For example, he* will match hello as well +as help. +

    +
  • Multiple words enclosed in double quotes are considered to be a +single keyword. For example, the quoted string "gene symbol" +is considered to be a single keyword composed of 11 characters, including a space. +The wildcard character is interpreted literally (i.e. as the '*' +character) if it appears within a quoted string. +

    +
  • Multiple keywords may be typed in one of the fields; this means to +search for any of the keywords in that field. For example, +typing fat sugar in the accepts field will search for +providers that map either fat or sugar to something else. +

    +
  • If keywords are typed in multiple fields, then only providers that +match keywords for all the fields will match. For example, +typing fat sugar into the accepts field, and +"weight gain" into the returns field will search for +providers that map either fat or sugar to weight gain. +

    +
=================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:01:20 1.2 @@ -16,21 +16,45 @@ Accepts Returns - - - + + +
Type any terms into the boxes above and press Search
-(for example type Hello into the Provider box) +(for example type 'hello' (without quotes) into the Provider box)

-

About Semantic MOBY   Help on Searching +


+ + + + + + + + + + + +
+ + CSHL + + NCGR + + NSF
+ + Cold Spring Harbor Laboratory + + National Center for Genome Resources + + National Science Foundation
From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KM9013059@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Modified Files: hello-world.n3 hello-world.rdf Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello hello-world.n3,1.1,1.2 hello-world.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3 2004/07/21 22:01:20 1.2 @@ -7,7 +7,7 @@ @prefix xsd: . ex:hello-world - a moby:Provider ; + a moby:Provider, exterms:GreetingProvider ; moby:name "Semantic MOBY Hello World provider" ; moby:oneLineDescription "Simple example of a Semantic MOBY provider" ; moby:operatesOn [ =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf 2004/07/21 22:01:20 1.2 @@ -8,20 +8,21 @@ xmlns:moby="http://www.semanticmoby.org/ontologies/core/" > + Simple example of a Semantic MOBY provider Semantic MOBY Hello World provider - - - - - + - + + + + + \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1Kfw012988@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Modified Files: URIInvestigator.java Added Files: KeywordQuery.java KeywordList.java KeywordFinder.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools KeywordQuery.java,NONE,1.1 KeywordList.java,NONE,1.1 KeywordFinder.java,NONE,1.1 URIInvestigator.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java 2004/07/15 20:27:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java 2004/07/21 22:01:19 1.2 @@ -216,7 +216,8 @@ // retrievable, but register the graph anyway // syncLog.warn("Unable to get Last-Modified date for " - + providerURI + "; ignoring"); + + providerURI + "; using current date"); + lastModifiedDate = new Date(); } catch (Throwable t) { From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1Knv013083@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageManager.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/21 22:01:20 1.2 @@ -9,6 +9,8 @@ import com.hp.hpl.jena.rdf.model.*; import com.hp.hpl.jena.shared.*; import com.hp.hpl.jena.vocabulary.*; +import java.sql.Connection; +import java.sql.SQLException; import java.util.*; /** @@ -60,7 +62,7 @@ { Model model = ((MOBYProviderImpl) provider).getUnderlying(); Model dbModel = null; - String uriString = provider.getURI(); + String uriString = provider.getResource().getURI(); Resource uri = model.createResource(uriString); try @@ -100,6 +102,12 @@ dbModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime()); } + // Add keywords associated with the provider + // + KeywordFinder finder = new KeywordFinder(provider, model); + addKeywords(provider.getResource().getURI(), + finder.getKeywords(), dbModel); + // Commit the transaction on the database model // dbModel.commit(); @@ -116,6 +124,73 @@ } } } + + private void addKeywords(String providerURI, KeywordList list, Model model) + throws StorageException + { + try + { + ModelRDB dbModel = (ModelRDB) model; + Connection conn = dbModel.getConnection().getConnection(); + + java.sql.Statement sql = conn.createStatement(); + + doAddKeywords(providerURI, list.getProviderKeywords(), "P", sql); + doAddKeywords(providerURI, list.getSubjectKeywords(), "S", sql); + doAddKeywords(providerURI, list.getObjectKeywords(), "O", sql); + + } + catch (Throwable t) + { + throw new StorageException(t); + } + } + + private void doAddKeywords(String providerURI, Iterator it, + String appliesTo, java.sql.Statement sql) + throws SQLException + { + while (it.hasNext()) + { + String keyword = it.next().toString(); + + StringBuffer sb = new StringBuffer(); + + sb.append("INSERT INTO MOBY_KEYWORD\n"); + sb.append(" (keyword, provider_uri, applies_to)\n"); + sb.append("values ('"); + sb.append(keyword.toLowerCase().trim()); + sb.append("', '"); + sb.append(providerURI); + sb.append("', '"); + sb.append(appliesTo); + sb.append("')"); + + String queryString = sb.toString(); + + sql.execute(queryString); + } + } + + private void removeKeywords(String providerURI, Model model) + throws StorageException + { + try + { + ModelRDB dbModel = (ModelRDB) model; + Connection conn = dbModel.getConnection().getConnection(); + + java.sql.Statement sql = conn.createStatement(); + + sql.execute("DELETE FROM MOBY_KEYWORD WHERE provider_uri = '" + + providerURI + "'"); + + } + catch (Throwable t) + { + throw new StorageException(t); + } + } /** * Remove all the statements registered by a given provider URI @@ -143,6 +218,10 @@ // ProviderRemover.remove(dbModel, providerURI); + // Remove keywords associated with the provider URI + // + removeKeywords(providerURI, dbModel); + // Commit the transaction on the database // dbModel.commit(); From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:41:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KH3013030@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Added Files: GreetingProvider.n3 GreetingProvider index.html Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies GreetingProvider.n3,NONE,1.1 GreetingProvider,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 17:42:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KKL013102@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Modified Files: web.xml Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml 2004/07/21 22:01:20 1.2 @@ -17,6 +17,13 @@ + ProviderEngagementServlet + engage-provider + Keyword search servlet + org.smoby.ref.servlets.ProviderEngagementServlet + + + HelloWorldServlet hello-world Hello World simple application @@ -64,6 +71,11 @@ + ProviderEngagementServlet + /engage-provider + + + HelloWorldServlet /examples/hello-world From gss at pub.open-bio.org Wed Jul 21 18:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 18:15:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZP58013212@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Modified Files: help1.png Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images help1.png,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png 2004/07/21 22:01:19 1.1 and /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png 2004/07/21 22:35:25 1.2 differ rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png: diff failed From gss at pub.open-bio.org Wed Jul 21 18:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 18:15:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZP6f013240@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/WebRoot Modified Files: help.html tech-overview.html index.html Removed Files: help1.jpg Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot help.html,1.2,1.3 tech-overview.html,1.1,1.2 index.html,1.2,1.3 help1.jpg,1.1,NONE =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:35:25 1.3 @@ -13,13 +13,13 @@ Semantic MOBY maintains a searchable repository of descriptions of providers of services that are available on the web. At the heart of these descriptions is the notion that providers map one type -of thing (what the provider accepts) to another type of thing (what -the provider returns). +of thing (the Subject) to another (the Object), or +vice versa.

-Providers, as well as things accepted and returned by providers, are -classified using web-accessible descriptions, and these descriptions +Providers, as well as subjects and objects, are +classified using web-accessible definitions (ontologies), and these definitions have keywords associated with them. For example, the following shows -a query for providers whose descriptions include the keyword "hello": +a query for providers whose definitions include the keyword "hello":

. @@ -28,7 +28,7 @@ Search hints
  • Keywords are not case sensitive, so HELLO means the -same thing as hello as does HeLloW. +same thing as hello as does HeLlO.

  • The wildcard character (*) can be used at the end of a keyword to match keywords that start with the characters before the wildcard. @@ -43,13 +43,13 @@

  • Multiple keywords may be typed in one of the fields; this means to search for any of the keywords in that field. For example, -typing fat sugar in the accepts field will search for +typing fat sugar in the Subject field will search for providers that map either fat or sugar to something else.

  • If keywords are typed in multiple fields, then only providers that match keywords for all the fields will match. For example, -typing fat sugar into the accepts field, and -"weight gain" into the returns field will search for +typing fat sugar into the Subject field, and +"weight gain" into the Object field will search for providers that map either fat or sugar to weight gain.

=================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html 2004/07/21 22:35:25 1.2 @@ -34,7 +34,11 @@ a Semantic MOBY provider, and should be examined first. -Graph
converter + + +Graph
converter + + An example that converts among various formats of OWL graphs. =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:35:25 1.3 @@ -13,8 +13,8 @@ - - + + @@ -45,15 +45,20 @@ NSF + CSHL + NCGR + NSF + + +
ProviderAcceptsReturns
SubjectObject
- - Cold Spring Harbor Laboratory - - National Center for Genome Resources - - National Science Foundation
+
+
+ +
+Under Construction - Pardon the Dust
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/help1.jpg,v: No such file or directory From gss at pub.open-bio.org Wed Jul 21 18:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Jul 21 18:15:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZPGs013260@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Modified Files: KeywordSearchServlet.java Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets KeywordSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:01:19 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:35:25 1.3 @@ -19,7 +19,7 @@ List returns = getKeywords("returns", request); startHTML(response, out); - if ((provider == null) && (accepts == null) && (returns == null)) + if ((provider.isEmpty()) && (accepts.isEmpty()) && (returns.isEmpty())) { showResultCount(-1, out); } From mwilkinson at pub.open-bio.org Mon Jul 26 13:09:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon Jul 26 12:49:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407261709.i6QH99FA005183@pub.open-bio.org> mwilkinson Mon Jul 26 13:09:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv5164/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: fixed a nasty bug that was preventing the proper registration of collection output services moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/09 00:21:53 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/26 17:09:09 1.3 @@ -102,23 +102,23 @@ sub insert_collection_input { my ($self, %args) = @_; my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ +# if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ # this should be dropped down into the mysql.pm module?? probably... $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); my $id=$self->dbh->{mysql_insertid}; return $id; - } +# } } sub insert_collection_output { my ($self, %args) = @_; my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ +# if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ # this should be dropped down into the mysql.pm module?? probably... $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); my $id=$self->dbh->{mysql_insertid}; return $id; - } +# } } sub insert_simple_input { From mwilkinson at pub.open-bio.org Tue Jul 27 18:56:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Jul 27 18:36:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407272256.i6RMuXo3012522@pub.open-bio.org> mwilkinson Tue Jul 27 18:56:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv12503/MOBY/Client Modified Files: CollectionArticle.pm Log Message: simples were being added to collections multiple times when creating a ServiceInstance from a DOM, rather than from parsing the XML manually. Fixed. RDF should now be somewhat more sensible. moby-live/Perl/MOBY/Client CollectionArticle.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/06/15 00:37:55 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/07/27 22:56:32 1.9 @@ -306,10 +306,7 @@ $self->articleName($articleName); my $objects = $dom->getElementsByTagName("Simple"); for my $n(0..$objects->getLength - 1){ - foreach my $child($objects->item($n)->getChildNodes){ - next unless $child->getNodeType == ELEMENT_NODE; - $self->addSimple(MOBY::Client::SimpleArticle->new(articleName=>$self->articleName, XML_DOM => $objects->item($n))); - } + $self->addSimple(MOBY::Client::SimpleArticle->new(articleName=>$self->articleName, XML_DOM => $objects->item($n))); } return $self; } From mwilkinson at pub.open-bio.org Wed Jul 28 18:55:14 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 18:34:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282255.i6SMtEH9016063@pub.open-bio.org> mwilkinson Wed Jul 28 18:55:13 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16045/RDF Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/RDF added to the repository moby-live/Perl/MOBY/RDF - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Wed Jul 28 18:56:59 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 18:36:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282256.i6SMuxUG016129@pub.open-bio.org> mwilkinson Wed Jul 28 18:56:59 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16114/RDF Added Files: ServiceInstanceRDF.pm InOutArticlesRDF.pm Log Message: added two new modules for generating RDF of MOBY-S Service Instances. This serves both the straight URL RDF documents, as well as (in a few minutes) the LSID metadata resolver service moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,NONE,1.1 InOutArticlesRDF.pm,NONE,1.1 From mwilkinson at pub.open-bio.org Wed Jul 28 18:59:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 18:39:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282259.i6SMxYGc016201@pub.open-bio.org> mwilkinson Wed Jul 28 18:59:34 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16178/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: clean up and add one more test moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.1,1.2 ServiceInstanceRDF.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:56:59 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:59:34 1.2 @@ -47,6 +47,7 @@ return 0 unless $args{'type'} && ( ($args{'type'} =~ /consumes/i) || ($args{'type'} =~ /produces/i) ); return 0 unless $args{'subject'} && (ref($args{'subject'}) =~ /rdf::core/i); return 0 unless $args{'araticles'} && (ref($args{'articles'}) =~ /array/i); + return 1 unless ${$args{'articles'}}[0]; # if there ARE no articles, this is a valid result! my $caller_is_obj = ref($caller); my $class = $caller_is_obj || $caller; @@ -134,13 +135,7 @@ my $namespaces = $ART->namespaces(); foreach (@{$namespaces}){ - # prime with base Object type "Class" - my $namespace = _addClassResource($model, NS, "$_", ''); - #my $type = $subject->new(RDF_NS,'type'); - #my $class = new RDF::Core::Resource(RDFS_NS,'Class'); - #my $statement = new RDF::Core::Statement($namespace, $type, $class); - #$model->addStmt($statement); - + my $namespace = _addClassResource($model, NS, "$_", ''); my $inNamespace = $article->new(MP, 'namespace_type'); my $statement = new RDF::Core::Statement($article, $inNamespace, $namespace); $model->addStmt($statement); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:56:59 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:59:34 1.2 @@ -69,16 +69,9 @@ _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title my $inputs = $service->input; - #my @inputs = @{$inputs}; my $outputs = $service->output; - #my @outputs = @{$outputs}; - -# THERE SHOULD BE A LOOP HERE TO TEST IF ANY INPUTS AT ALL - - - #foreach my $IN(@inputs){ my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', @@ -86,9 +79,6 @@ articles => $inputs, ); - #} -##################################################### - my $OutputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'produces', From mwilkinson at pub.open-bio.org Wed Jul 28 19:00:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 18:39:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282300.i6SN09fA016280@pub.open-bio.org> mwilkinson Wed Jul 28 19:00:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv16257 Modified Files: INSTALL MANIFEST Log Message: adding new modules to the manifest. removing old outdated installation documents moby-live/Perl INSTALL,1.1,1.2 MANIFEST,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/INSTALL 2003/06/10 17:12:52 1.1 +++ /home/repository/moby/moby-live/Perl/INSTALL 2004/07/28 23:00:09 1.2 @@ -1,33 +1,15 @@ ----------- CLIENT CONFIGURATION ---------- -If you wish to conect, by default, to anything other than -the MOBY Central registry running at the Canadian -Bioinformatics Resource (mobycentral.cbr.nrc.ca) then -you should set the following environment variables: +perl Makefile.PL +make +make install -MOBY_SERVER=http://your.favorite.server/cgi-bin/serverscriptname.pl -MOBY_URI=http://your.favorite.server/PathTo/MOBY -for example, to connect by default to a local copy of -the registry it might look like this: +MOST PEOPLE CAN STOP READING NOW! -MOBY_SERVER=http://localhost/cgi-bin/MOBY-Central.pl -MOBY_URI=http://localhost/MOBY/Central -=========================================== +For details on how to configure your own MOBY Central +registry, should you want to set one up (you DO NOT +need to set up a registry to acess nor service MOBY-S +Services) please visit the "Installing a Local Registy" +link on the biomoby.org homepage. -------- SERVER CONFIGURATION ------------ -If you are installing a local copy of MOBY Central -you will need to set some additional environment -variables in your httpd.conf file to tell the modules -where your mysql installation is. These are -configured using the apache SetEnv directive as follows: - -SetEnv MOBY_CENTRAL_DBNAME mobycentral -SetEnv MOBY_CENTRAL_DBPASS yourpassword -SetEnv MOBY_CENTRAL_DBPORT 3306 -SetEnv MOBY_CENTRAL_DBUSER mobyusername -SetEnv MOBY_CENTRAL_URL localhost - -(don't forget to restart your server...) -========================================== - +Mark =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MANIFEST 2004/06/24 22:32:38 1.11 +++ /home/repository/moby/moby-live/Perl/MANIFEST 2004/07/28 23:00:09 1.12 @@ -45,3 +45,5 @@ MOBY/lsid/authority/RelationshipResolver.pm MOBY/lsid/authority/ServiceInstanceResolver.pm MOBY/lsid/authority/ServiceResolver.pm +MOBY/RDF/ServiceInstanceRDF.pm +MOBY/RDF/InOutArticlesRDF.pm From mwilkinson at pub.open-bio.org Wed Jul 28 19:08:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 18:47:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282308.i6SN89Nu016375@pub.open-bio.org> mwilkinson Wed Jul 28 19:08:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16356/RDF Modified Files: ServiceInstanceRDF.pm Log Message: RDF/ServiceInstanceRDF.pm moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:59:34 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:08:09 1.3 @@ -1,6 +1,5 @@ package MOBY::RDF::ServiceInstanceRDF; use strict; -use lib '../../'; use MOBY::RDF::InOutArticlesRDF; require Exporter; our @ISA = qw(Exporter); @@ -50,7 +49,7 @@ sub build { my ($self) = @_; - my $service = $self->service; + my $service = $self->service_instance; my $model = $self->model; my $Bag = new RDF::Core::Resource(RDF_NS,'Bag'); From mwilkinson at pub.open-bio.org Wed Jul 28 19:12:11 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 18:51:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282312.i6SNCBj7016462@pub.open-bio.org> mwilkinson Wed Jul 28 19:12:11 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16439/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: shuffling subroutines around moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.2,1.3 ServiceInstanceRDF.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:59:34 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:12:11 1.3 @@ -141,4 +141,59 @@ $model->addStmt($statement); } } + + + +sub _addResource { + my ($model, $ns, $predicate, $subject, $ons, $object) = @_; + + $predicate = $subject->new($ns, $predicate); + $object = new RDF::Core::Resource($ons, $object); + my $statement = new RDF::Core::Statement($subject, $predicate, $object); + $model->addStmt($statement); + +} + + +# these should also be stripped out into their own module +sub _addClassResource { + my ($model, $ns, $thing, $def) = @_; + my ($subject, $statement, $class, $label, $type); + + $label = ($thing =~ /urn:lsid.*:(\S+)$/)?$1:$thing; + + unless (ref($thing) =~ /RDF/){ + $subject = new RDF::Core::Resource($ns, $thing); + } + + $type = $subject->new(RDF_NS,'type'); + $class = new RDF::Core::Resource(RDFS_NS,'Class'); + $statement = new RDF::Core::Statement($subject, $type, $class); + $model->addStmt($statement); + + $type = $subject->new(RDFS_NS,'label'); + $label = new RDF::Core::Literal($label,"en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject unless $def; + + $type = $subject->new(RDFS_NS,'comment'); + $label = new RDF::Core::Literal($def, "en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject; +} + +sub _addClassLiteral { + my ($model, $pns, $subject, $predicate, $value) = @_; + + $predicate = $subject->new($pns, $predicate); + $value = new RDF::Core::Literal($value, "en", "http://www.w3.org/2001/XMLSchema#string"); + my $statement = new RDF::Core::Statement($subject, $predicate, $value); + $model->addStmt($statement); + +} + 1; \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:08:09 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:12:11 1.4 @@ -88,4 +88,55 @@ } +# these should be stripped out into their own module... +sub _addResource { + my ($model, $ns, $predicate, $subject, $ons, $object) = @_; + + $predicate = $subject->new($ns, $predicate); + $object = new RDF::Core::Resource($ons, $object); + my $statement = new RDF::Core::Statement($subject, $predicate, $object); + $model->addStmt($statement); + +} + +sub _addClassResource { + my ($model, $ns, $thing, $def) = @_; + my ($subject, $statement, $class, $label, $type); + + $label = ($thing =~ /urn:lsid.*:(\S+)$/)?$1:$thing; + + unless (ref($thing) =~ /RDF/){ + $subject = new RDF::Core::Resource($ns, $thing); + } + + $type = $subject->new(RDF_NS,'type'); + $class = new RDF::Core::Resource(RDFS_NS,'Class'); + $statement = new RDF::Core::Statement($subject, $type, $class); + $model->addStmt($statement); + + $type = $subject->new(RDFS_NS,'label'); + $label = new RDF::Core::Literal($label,"en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject unless $def; + + $type = $subject->new(RDFS_NS,'comment'); + $label = new RDF::Core::Literal($def, "en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject; +} + +sub _addClassLiteral { + my ($model, $pns, $subject, $predicate, $value) = @_; + + $predicate = $subject->new($pns, $predicate); + $value = new RDF::Core::Literal($value, "en", "http://www.w3.org/2001/XMLSchema#string"); + my $statement = new RDF::Core::Statement($subject, $predicate, $value); + $model->addStmt($statement); + +} + 1; \ No newline at end of file From mwilkinson at pub.open-bio.org Wed Jul 28 19:41:39 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 19:21:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282341.i6SNfdka016576@pub.open-bio.org> mwilkinson Wed Jul 28 19:41:39 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16557/RDF Modified Files: InOutArticlesRDF.pm Log Message: adding a class variable counter for the various node factories so that all inputs in the database don't end up getting added to a single service in the RDF >>grin<< moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:12:11 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:41:39 1.4 @@ -1,6 +1,7 @@ package MOBY::RDF::InOutArticlesRDF; use strict; use RDF::Core::NodeFactory; +use RDF::Core::Statement; require Exporter; our @ISA = qw(Exporter); @@ -14,6 +15,35 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +{ + my $inputcounter = 1; + my $outputcounter = 1; + my $simplecounter = 1; + my $collectioncounter = 1; + + sub nextinput { + ++$inputcounter; + $inputcounter = 1 if $inputcounter==100000; + return $inputcounter; + } + sub nextoutput { + ++$outputcounter; + $outputcounter = 1 if $outputcounter==100000; + return $outputcounter; + } + sub nextsimple { + ++$simplecounter; + $simplecounter = 1 if $simplecounter==100000; + return $simplecounter; + } + sub nextcollection { + ++$collectioncounter; + $collectioncounter = 1 if $collectioncounter==100000; + return $collectioncounter; + } + +} + sub type { my ($self, @args) = @_; $args[0] && ($self->{type} = $args[0]); @@ -46,7 +76,7 @@ return 0 unless $args{'model'} && (ref($args{'model'}) =~ /rdf::core/i); return 0 unless $args{'type'} && ( ($args{'type'} =~ /consumes/i) || ($args{'type'} =~ /produces/i) ); return 0 unless $args{'subject'} && (ref($args{'subject'}) =~ /rdf::core/i); - return 0 unless $args{'araticles'} && (ref($args{'articles'}) =~ /array/i); + return 0 unless $args{'articles'} && (ref($args{'articles'}) =~ /array/i); return 1 unless ${$args{'articles'}}[0]; # if there ARE no articles, this is a valid result! my $caller_is_obj = ref($caller); @@ -61,10 +91,10 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &inputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &outputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &simplecounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &collectioncounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); @@ -91,8 +121,9 @@ my @articles = $self->articles; my $Bag = $self->{Bag}; - my $li = 1; + my $li = 0; foreach my $IN(@articles){ + ++$li; my $LI = $Thingy->new(RDF_NS, "_$li"); my $input = $self->{inputfactory}->newResource; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); @@ -111,9 +142,10 @@ _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; my $simps = $IN->Simples; + my $lli=0; foreach my $simp(@{$simps}){ - my $li = 1; - my $LI = $input->new(RDF_NS, "_$li"); + ++$lli; + my $LI = $input->new(RDF_NS, "_$lli"); my $collection_member = $self->{inputfactory}->newResource; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); From mwilkinson at pub.open-bio.org Wed Jul 28 19:45:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 19:25:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282345.i6SNjXjY016644@pub.open-bio.org> mwilkinson Wed Jul 28 19:45:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16625/RDF Modified Files: InOutArticlesRDF.pm Log Message: call the method, not the variable moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:41:39 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:45:33 1.5 @@ -91,10 +91,10 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &inputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &outputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &simplecounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &collectioncounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &nextinput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &nextoutput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &nextsimple(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &nextcollection(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); From mwilkinson at pub.open-bio.org Wed Jul 28 20:22:21 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 20:02:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407290022.i6T0MLaF016803@pub.open-bio.org> mwilkinson Wed Jul 28 20:22:21 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16780/MOBY/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: ups. Got my class variables wrong. Now it increments properly to associate inputs with the correct services moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.5,1.6 ServiceInstanceRDF.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:45:33 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 00:22:21 1.6 @@ -16,30 +16,22 @@ use constant DC => 'http://purl.org/dc/elements/1.1/'; { - my $inputcounter = 1; - my $outputcounter = 1; - my $simplecounter = 1; - my $collectioncounter = 1; + my $inputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $outputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $simplefactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $collectionfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); sub nextinput { - ++$inputcounter; - $inputcounter = 1 if $inputcounter==100000; - return $inputcounter; + return $inputfactory->newResource } sub nextoutput { - ++$outputcounter; - $outputcounter = 1 if $outputcounter==100000; - return $outputcounter; + return $outputfactory->newResource } sub nextsimple { - ++$simplecounter; - $simplecounter = 1 if $simplecounter==100000; - return $simplecounter; + return $simplefactory->newResource } sub nextcollection { - ++$collectioncounter; - $collectioncounter = 1 if $collectioncounter==100000; - return $collectioncounter; + return $collectionfactory->newResource } } @@ -91,14 +83,14 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &nextinput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &nextoutput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &nextsimple(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &nextcollection(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); - - my $Thingy = $self->{inputfactory}->newResource; # create a bnode + my $Thingy; + if ($self->type eq 'consumes'){ + $Thingy = &nextinput; # create a bnode + } else { + $Thingy = &nextoutput; # create a bnode + } my $predicate = $subject->new(MP,$self->type); # 'consumes' or 'produces' my $statement = new RDF::Core::Statement($subject, $predicate, $Thingy); $model->addStmt($statement); @@ -125,13 +117,12 @@ foreach my $IN(@articles){ ++$li; my $LI = $Thingy->new(RDF_NS, "_$li"); - my $input = $self->{inputfactory}->newResource; + my $input = &nextsimple; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); $model->addStmt($statement); # # - - + if ($IN->isSimple){ &_addSimple($model, $input, $IN); } else { # COLLECTION @@ -146,7 +137,7 @@ foreach my $simp(@{$simps}){ ++$lli; my $LI = $input->new(RDF_NS, "_$lli"); - my $collection_member = $self->{inputfactory}->newResource; + my $collection_member = &nextcollection; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:12:11 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 00:22:21 1.5 @@ -1,6 +1,8 @@ package MOBY::RDF::ServiceInstanceRDF; use strict; use MOBY::RDF::InOutArticlesRDF; +use RDF::Core::Statement; + require Exporter; our @ISA = qw(Exporter); our @EXPORT_OK = qw(); From mwilkinson at pub.open-bio.org Wed Jul 28 20:36:55 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Jul 28 20:16:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407290036.i6T0atVS016900@pub.open-bio.org> mwilkinson Wed Jul 28 20:36:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv16881/MOBY/lsid/authority Modified Files: ServiceInstanceResolver.pm Log Message: the LSID resolver for service instance LSID's now uses the same modules as the RESOURCES script, and should output identically formatted RDF moby-live/Perl/MOBY/lsid/authority ServiceInstanceResolver.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm 2004/01/15 20:59:38 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm 2004/07/29 00:36:54 1.4 @@ -5,6 +5,35 @@ use XML::DOM; use MOBY::lsid::authority::RDFConfigure qw(:all); use MOBY::Client::Central; +use MOBY::RDF::ServiceInstanceRDF; + +use RDF::Core; +use RDF::Core::Model; +use RDF::Core::Literal; +use RDF::Core::Statement; +use RDF::Core::Model::Serializer; +use RDF::Core::Storage::Memory; +use RDF::Core::Constants qw(:xml :rdf :rdfs); +use constant OBJ => 'http://biomoby.org/RESOURCES/MOBY-S/Objects#'; +use constant SRV => 'http://biomoby.org/RESOURCES/MOBY-S/Services#'; +use constant NS => 'http://biomoby.org/RESOURCES/MOBY-S/Namespaces#'; +use constant MP => 'http://biomoby.org/RESOURCES/MOBY-S/Predicates#'; +use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; +use constant DC => 'http://purl.org/dc/elements/1.1/'; + +sub xmlNamespaces { + return { + RDF_NS() => 'rdf', + RDFS_NS() => 'rdfs', + OBJ() => 'mobyObject', + NS() => 'mobyNamespace', + SRV() => 'mobyService', + MP() => 'mobyPred', + SI() => 'serviceInstances', + DC() => 'dc', + } +} + @ISA = qw(Exporter); @EXPORT_OK = qw( @@ -14,8 +43,21 @@ resolve_ServiceInstance )]); +sub _serialize { + my ($model) = @_; + my $xml = ''; + + my $serializer = new RDF::Core::Model::Serializer( + Model=>$model, + Output=>\$xml, + getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! + ); + $serializer->serialize; + print "$xml\n"; +} sub resolve_ServiceInstance { + my ($ls) = @_; my $lsid= LS::ID->new($ls)->canonical; unless ($lsid) { @@ -37,175 +79,20 @@ unless ($si && ${$si}[0]){ _die('UNKNOWN_LSID'); } - my $service = shift(@{$si}); - # LSID is now fully validated. Carry on with metadata. - $RDF_PREFIX?1:1; - $mdata= $RDF_PREFIX; - - $mdata.= rdfLiteral( - $lsid->as_string, - 'rdf:type', # rdf:Type - 'i3csp:bioMobyService' - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:name', # i3c:Name - $service->name - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:title', # dc:Title - $service->name - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:label', # dc:Label - $service->name - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:publishedBy', # i3d:publishedBy - $service->authority - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:authoritative', # i3c:authoritative - $service->authoritative - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:description', # i3c:description - $service->description - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:endpoint', # i3c:endpoint - $service->URL - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:contributor', # dc:contributor - $service->contactEmail - ); - - $mdata.= rdfResource( - $lsid->as_string, - 'i3csp:performsTask', # i3csp:performsTask - 'urn:lsid:biomoby.org:servicetype:'.($service->type) - ); - - - my $inputs = $service->input; - my @inputs = @{$inputs}; + my $storage = new RDF::Core::Storage::Memory; + my $model = new RDF::Core::Model (Storage => $storage); - my $outputs = $service->output; - my @outputs = @{$outputs}; - - $mdata .= rdfBnode( - $lsid->as_string, - 'i3csp:primaryInput', # primaryInput bnode - 'primaryInput' - ); - my $in=0; - foreach (@inputs){ - ++$in; - $mdata .= rdfBnodeBnode( - 'primaryInput', - 'i3csp:primaryParameter', # primaryParameter bnode - "primaryParameter$in" - ); - $mdata .= rdfBnodeLiteral( - "primaryParameter$in", - 'i3csp:parameterName', - $_->articleName - ); - if ($_->isSimple){ - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterType', - 'i3csp:mobySimpleType' - ); - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($_->objectType) - ); - } else { - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterType', - 'i3csp:mobyCollectionType' - ); - my $simps = $_->Simples; - foreach my $simp(@{$simps}){ - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($simp->objectType) - ); - } - } - } - - $mdata .= rdfBnode( - $lsid->as_string, - 'i3csp:primaryOutput', # primaryInput bnode - 'primaryOutput' - ); - my $out= $in; # switch for readability - foreach (@outputs){ - ++$out; - $mdata .= rdfBnodeBnode( - 'primaryOutput', - 'i3csp:primaryParameter', # primaryParameter bnode - "primaryParameter$out" - ); - $mdata .= rdfBnodeLiteral( - "primaryParameter$out", - 'i3csp:parameterName', - $_->articleName - ); - if ($_->isSimple){ - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterType', - 'i3csp:mobySimpleType' - ); - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($_->objectType) - ); - } else { - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterType', - 'i3csp:mobyCollectionType' - ); - my $simps = $_->Simples; - foreach my $simp(@{$simps}){ - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($simp->objectType) - ); - } - } + foreach my $service(@{$si}){ + my $ServInstRDF = MOBY::RDF::ServiceInstanceRDF->new( + model => $model, + service_instance => $service, + ); } - - # +++++++++++ now we need the secondaries ++++++++ - $mdata.= $RDF_SUFFIX; - $RDF_SUFFIX?1:1; - - unless ($mdata) { - _die ('NO_METADATA_AVAILABLE'); - } - return $mdata; + print header(-type => 'application/rdf+xml', -expires => 'now'); + _serialize($model); + exit 1; } + +1; From mwilkinson at pub.open-bio.org Thu Jul 29 12:11:41 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 11:51:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407291611.i6TGBfMA019343@pub.open-bio.org> mwilkinson Thu Jul 29 12:11:40 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv19324/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: adding support for secondaries into the RDF generating routines moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 00:22:21 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 16:11:40 1.7 @@ -15,11 +15,13 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; -{ +{ # these need to be class variables, since this module is loaded multiple times, but the newResouce counter has to increment nevertheless. + my $inputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $outputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $simplefactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $collectionfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $secondaryfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:secondary', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); sub nextinput { return $inputfactory->newResource @@ -33,9 +35,14 @@ sub nextcollection { return $collectionfactory->newResource } + sub nextsecondary { + return $secondaryfactory->newResource + } } + + sub type { my ($self, @args) = @_; $args[0] && ($self->{type} = $args[0]); @@ -116,7 +123,7 @@ my $li = 0; foreach my $IN(@articles){ ++$li; - my $LI = $Thingy->new(RDF_NS, "_$li"); + my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc my $input = &nextsimple; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); $model->addStmt($statement); @@ -125,18 +132,18 @@ if ($IN->isSimple){ &_addSimple($model, $input, $IN); - } else { # COLLECTION + } elsif ($IN->isCollection) { # COLLECTION - is just a bag of simples my $type = $input->new(RDF_NS,'type'); my $statement = new RDF::Core::Statement($input, $type, $Bag); $model->addStmt($statement); # - _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; + _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; # the bag has an articlename my $simps = $IN->Simples; my $lli=0; foreach my $simp(@{$simps}){ ++$lli; - my $LI = $input->new(RDF_NS, "_$lli"); + my $LI = $input->new(RDF_NS, "_$lli"); # nodes - need to be numbered :_1, :_2, etc; these connect to the individual simples my $collection_member = &nextcollection; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); @@ -144,6 +151,10 @@ &_addSimple($model, $collection_member, $simp); } + } elsif ($IN->isSecondary) { + &_addSecondary($model, $input, $IN); + } else { + print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; } } } @@ -166,6 +177,27 @@ } +#| secondary_input_id | int(10) unsigned | | PRI | NULL | auto_increment | +#| default_value | text | YES | | NULL | | +#| maximum_value | decimal(10,0) | YES | | NULL | | +#| minimum_value | decimal(10,0) | YES | | NULL | | +#| enum_value | text | YES | | NULL | | +#| datatype | enum('String','Integer','DateTime','Float') | YES | | NULL | | +#| article_name | varchar(255) | YES | | NULL | | +#| service_instance_id | int(10) unsigned | | | 0 | | +sub _addSecondary { + my ($model, $article, $ART) = @_; # (RDF::COre::Model, $RDF::Core::Resource, $MOBY::Client::SimpleArticle) + _addClassLiteral($model, MP, $article, 'article_name', $ART->articleName) if $ART->articleName; + _addClassLiteral($model, MP, $article, 'default_value', $ART->default) if $ART->default; + _addClassLiteral($model, MP, $article, 'datatype', $ART->datatype) if $ART->datatype; + _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; + _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; + my @enums = $ART->enum; + foreach (@enums){ + _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; + } + +} sub _addResource { my ($model, $ns, $predicate, $subject, $ons, $object) = @_; From mwilkinson at pub.open-bio.org Thu Jul 29 13:49:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 13:28:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407291749.i6THnIfq019710@pub.open-bio.org> mwilkinson Thu Jul 29 13:49:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv19691/MOBY/lsid/authority Modified Files: metadata.pl Log Message: LSID's are no longer case sensitive in the new LS::* stack from IBM moby-live/Perl/MOBY/lsid/authority metadata.pl,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl 2004/01/15 20:59:38 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl 2004/07/29 17:49:18 1.5 @@ -28,13 +28,13 @@ use MOBY::lsid::authority::ServiceInstanceResolver qw(:all); my %known_types = ( # switch on/off various LSID-namespace resolvers. - 'namespacetype' => 1, - 'objectclass' => 1, - 'servicetype' => 1, - 'servicerelation' => 1, - 'objectrelation' => 1, - 'serviceinstance' => 1, - 'rdfpredicate' => 1, + 'NamespaceType' => 1, + 'ObjectClass' => 1, + 'ServiceType' => 1, + 'ServiceRelation' => 1, + 'ObjectRelation' => 1, + 'ServiceInstance' => 1, + 'MOBYSPredicate' => 1, ); MetaData(); @@ -68,13 +68,13 @@ _die("UNKNOWN_LSID"); } - return resolve_namespacetype($namespacedb,$lsid) if $1 eq "namespacetype"; - return resolve_classtype($objectdb,$lsid) if $1 eq "objectclass"; - return resolve_servicetype($servicedb,$lsid) if $1 eq "servicetype"; - return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "objectrelation"; - return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "servicerelation"; - return resolve_mobyPredicate($lsid) if $1 eq "rdfpredicate"; - return resolve_ServiceInstance($lsid) if $1 eq "serviceinstance"; + return resolve_namespacetype($namespacedb,$lsid) if $1 =~ /namespacetype/i; + return resolve_classtype($objectdb,$lsid) if $1 =~ /objectclass/i; + return resolve_servicetype($servicedb,$lsid) if $1 =~ /servicetype/i; + return resolve_relationshiptype($relationshipdb,$lsid) if $1 =~ /objectrelation/i; + return resolve_relationshiptype($relationshipdb,$lsid) if $1 =~ /servicerelation/i; + return resolve_mobyPredicate($lsid) if $1 =~ /rdfpredicate/i; + return resolve_ServiceInstance($lsid) if $1 =~ /serviceinstance/i; } From mwilkinson at pub.open-bio.org Thu Jul 29 17:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 17:33:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrsHH020286@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY/Client Modified Files: Central.pm Registration.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY/Client Central.pm,1.76,1.77 Registration.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.76 retrieving revision 1.77 diff -u -r1.76 -r1.77 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/06/16 01:15:30 1.76 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/29 21:53:54 1.77 @@ -1654,10 +1654,12 @@ my $id = &_nodeTextContent($Object, 'id'); my $success = &_nodeTextContent($Object, 'success'); my $message = &_nodeTextContent($Object, 'message'); + my $RDF = &_nodeTextContent($Object, 'RDF'); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, registration_id => $id, + RDF => $RDF, id => $id); return $reg; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2003/06/06 00:45:47 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/07/29 21:53:54 1.5 @@ -81,6 +81,7 @@ success => [0, 'read/write'], message => ["OK", 'read/write'], registration_id => [undef, 'read/write'], + RDF => [undef, 'read/write'], ); #_____________________________________________________________ From mwilkinson at pub.open-bio.org Thu Jul 29 17:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 17:33:32 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrsB1020305@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 00:22:21 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 21:53:54 1.6 @@ -15,6 +15,33 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +sub xmlNamespaces { + return { + RDF_NS() => 'rdf', + RDFS_NS() => 'rdfs', + OBJ() => 'mobyObject', + NS() => 'mobyNamespace', + SRV() => 'mobyService', + MP() => 'mobyPred', + SI() => 'serviceInstances', + DC() => 'dc', + } +} + + +sub serialize { + my ($model) = @_; + my $xml = ''; + + my $serializer = new RDF::Core::Model::Serializer( + Model=>$model, + Output=>\$xml, + getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! + ); + $serializer->serialize; + return $xml; +} + sub model { my ($self, @args) = @_; $args[0] && ($self->{model} = $args[0]); From mwilkinson at pub.open-bio.org Thu Jul 29 17:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 17:33:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrspw020263@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY Modified Files: Central.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY Central.pm,1.133,1.134 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.133 retrieving revision 1.134 diff -u -r1.133 -r1.134 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/12 00:39:37 1.133 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 21:53:53 1.134 @@ -22,6 +22,14 @@ use MOBY::secondary_input; use MOBY::central_db_connection; use MOBY::Config; +use MOBY::RDF::ServiceInstanceRDF; +use RDF::Core; +use RDF::Core::Model; +use RDF::Core::Literal; +use RDF::Core::Statement; +use RDF::Core::Model::Serializer; +use RDF::Core::Storage::Memory; +use RDF::Core::Constants qw(:xml :rdf :rdfs); my $debug = 0; @@ -153,11 +161,15 @@ my $id = $details->{id}; my $success = $details->{success}; my $message = $details->{message}; + my $RDF = ""; + $RDF = $details->{RDF}; + return " $id $success + "; } @@ -1149,7 +1161,36 @@ return &_error("Registration Failed During SECONDARY Article Registration: $msg","") unless ($success==1); } - return &_success("Registration successful", $SVC->service_instance_id); + # we're going to do a findService here to find the service that we just created + # and use the resulting XML to create a MOBY::Client::ServiceInstance object + # that we can then use to retrieve the RDF for that service signature. + # this is roundabout, I agree, but it is the most re-usable way to go at + # the moment. + + my ($si, $reg) = &findService(qw{ + + + $AuthURI; + $serviceName; + + "}); + unless ($si){ + $SVC->DELETE_THYSELF; + return &_error("Registration Failed - newly registered service could not be discovered",""); + } + my $service = shift @{$si}; + unless ($service){ + $SVC->DELETE_THYSELF; + return &_error("Registration Failed - newly registered service could not be discovered",""); + } + + my $services = MOBY::Client::Central::_parseServices('', '', $service); + my $service_instance = shift @{$services}; + my $storage = new RDF::Core::Storage::Memory; + my $model = new RDF::Core::Model (Storage => $storage); + my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(model => $model, service_instance => $service_instance); + my $RDF_XML = $RDF_MODEL->serialize; + return &_success("Registration successful", $SVC->service_instance_id, $RDF_XML); } sub _registerArticles { @@ -2977,11 +3018,12 @@ } sub _success { - my ($message, $id) = @_; + my ($message, $id, $RDF) = @_; my $reg = &Registration({ success => 1, message => "$message", id => "$id", + RDF => $RDF, }); return $reg; } From gss at pub.open-bio.org Thu Jul 29 19:30:12 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:09:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292330.i6TNUCwS020618@pub.open-bio.org> gss Thu Jul 29 19:30:12 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv20593/src/org/smoby/parser/test Modified Files: Test.java Log Message: Removed unused import statement moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java 2004/06/16 23:29:32 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java 2004/07/29 23:30:12 1.3 @@ -4,7 +4,6 @@ import java.util.*; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.parser.*; import com.hp.hpl.jena.rdf.model.*; From gss at pub.open-bio.org Thu Jul 29 19:31:44 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:11:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292331.i6TNViBj020675@pub.open-bio.org> gss Thu Jul 29 19:31:44 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv20626/src/org/smoby/graph/impl Removed Files: MOBYProviderSetImpl.java MOBYProviderImpl.java MOBYResizableCollectionImpl.java MOBYUnorderedCollectionImpl.java MOBYDateConstraintImpl.java MOBYPropertyValueStatementImpl.java MOBYDocumentImpl.java MOBYLiteralImpl.java MOBYOntologyImpl.java MOBYEnumerationImpl.java MOBYSubjectImpl.java MOBYGraphNodeImpl.java MOBYObjectFactory.java MOBYFixedCollectionImpl.java MOBYIntegerConstraintImpl.java MOBYObjectImpl.java MOBYPropertyValueConstraintImpl.java MOBYPropertyValueImpl.java MOBYMappingElementImpl.java MOBYGraphImpl.java MOBYNonPositiveIntegerConstraintImpl.java MOBYNumericConstraintImpl.java MOBYNonNegativeIntegerConstraintImpl.java MOBYOrderedCollectionImpl.java MOBYResourceImpl.java MOBYDescriptorImpl.java MOBYCollectionImpl.java MOBYSingleElementImpl.java Log Message: No longer separate graph interfaces from classes moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderSetImpl.java,1.1,NONE MOBYProviderImpl.java,1.2,NONE MOBYResizableCollectionImpl.java,1.2,NONE MOBYUnorderedCollectionImpl.java,1.2,NONE MOBYDateConstraintImpl.java,1.1,NONE MOBYPropertyValueStatementImpl.java,1.1,NONE MOBYDocumentImpl.java,1.2,NONE MOBYLiteralImpl.java,1.1,NONE MOBYOntologyImpl.java,1.2,NONE MOBYEnumerationImpl.java,1.2,NONE MOBYSubjectImpl.java,1.2,NONE MOBYGraphNodeImpl.java,1.2,NONE MOBYObjectFactory.java,1.3,NONE MOBYFixedCollectionImpl.java,1.2,NONE MOBYIntegerConstraintImpl.java,1.1,NONE MOBYObjectImpl.java,1.2,NONE MOBYPropertyValueConstraintImpl.java,1.1,NONE MOBYPropertyValueImpl.java,1.1,NONE MOBYMappingElementImpl.java,1.2,NONE MOBYGraphImpl.java,1.2,NONE MOBYNonPositiveIntegerConstraintImpl.java,1.1,NONE MOBYNumericConstraintImpl.java,1.1,NONE MOBYNonNegativeIntegerConstraintImpl.java,1.1,NONE MOBYOrderedCollectionImpl.java,1.2,NONE MOBYResourceImpl.java,1.1,NONE MOBYDescriptorI! mpl.java,1.2,NONE MOBYCollectionImpl.java,1.2,NONE MOBYSingleElementImpl.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYProviderSetImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYProviderImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYResizableCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYUnorderedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDateConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueStatementImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDocumentImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYLiteralImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYOntologyImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYEnumerationImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYSubjectImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYGraphNodeImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYObjectFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYFixedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYObjectImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYMappingElementImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYGraphImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNonPositiveIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNumericConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNonNegativeIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYOrderedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYResourceImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDescriptorImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYSingleElementImpl.java,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 19:33:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:13:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292333.i6TNXxG9020829@pub.open-bio.org> gss Thu Jul 29 19:33:59 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv20716/src/org/smoby/graph Modified Files: MOBYDocument.java MOBYLiteral.java MOBYResource.java MOBYFixedCollection.java MOBYResizableCollection.java MOBYSingleElement.java MOBYPropertyValueConstraint.java MOBYPropertyValueStatement.java MOBYEnumeration.java MOBYProvider.java MOBYPropertyValue.java MOBYOntology.java MOBYProviderSet.java MOBYMappingElement.java MOBYDescriptor.java MOBYOrderedCollection.java MOBYCollection.java MOBYUnorderedCollection.java MOBYGraph.java MOBYGraphNode.java MOBYObject.java MOBYSubject.java MOBYPropertyValueException.java Added Files: MOBYIntegerConstraint.java MOBYDateConstraint.java MOBYNonNegativeIntegerConstraint.java MOBYNumericConstraint.java MOBYNonPositiveIntegerConstraint.java Log Message: No longer separate graph interfaces from classes moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYIntegerConstraint.java,NONE,1.1 MOBYDateConstraint.java,NONE,1.1 MOBYNonNegativeIntegerConstraint.java,NONE,1.1 MOBYNumericConstraint.java,NONE,1.1 MOBYNonPositiveIntegerConstraint.java,NONE,1.1 MOBYDocument.java,1.1,1.2 MOBYLiteral.java,1.1,1.2 MOBYResource.java,1.1,1.2 MOBYFixedCollection.java,1.1,1.2 MOBYResizableCollection.java,1.1,1.2 MOBYSingleElement.java,1.1,1.2 MOBYPropertyValueConstraint.java,1.1,1.2 MOBYPropertyValueStatement.java,1.1,1.2 MOBYEnumeration.java,1.1,1.2 MOBYProvider.java,1.1,1.2 MOBYPropertyValue.java,1.1,1.2 MOBYOntology.java,1.1,1.2 MOBYProviderSet.java,1.1,1.2 MOBYMappingElement.java,1.1,1.2 MOBYDescriptor.java,1.2,1.3 MOBYOrderedCollection.java,1.1,1.2 MOBYCollection.java,1.1,1.2 MOBYUnorderedCollection.java,1.1,1.2 MOBYGraph.java,1.1,1.2 MOBYGraphNode.java,1.1,1.2 MOBYObject.java,1.1,1.2 MOBYSubject.java,1.1,1.2 MOBYPropertyValueException.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,15 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents a document to be incorporated into + * This class represents a document to be incorporated into * the S-MOBY metadata repository. */ -public interface MOBYDocument extends MOBYDescriptor +public abstract class MOBYDocument extends MOBYDescriptor { + public MOBYDocument(Resource resource, Model underlying) + { + super(resource, underlying); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java 2004/07/29 23:33:59 1.2 @@ -1,7 +1,24 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.Literal; -public interface MOBYLiteral extends MOBYPropertyValue +public class MOBYLiteral extends MOBYPropertyValue { - public String getStringValue(); -} \ No newline at end of file + private String stringValue; + + public MOBYLiteral(String stringValue) { + this.stringValue = stringValue; + } + + public String getStringValue() { + return stringValue; + } + + public boolean isLiteral() { + return true; + } + + public boolean isResource() { + return false; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,29 @@ package org.smoby.graph; +import org.smoby.graph.*; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYResource extends MOBYPropertyValue +public class MOBYResource extends MOBYPropertyValue { - public String getResourceURI(); - public boolean isBlank(); + private Resource resourceValue; + + public MOBYResource(Resource resourceValue) { + this.resourceValue = resourceValue; + } + + public String getResourceURI() { + return resourceValue.getURI(); + } + + public boolean isLiteral() { + return false; + } + + public boolean isResource() { + return true; + } + + public boolean isBlank() { + return resourceValue.isAnon(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,20 @@ package org.smoby.graph; +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface representing unordered, fixed sized collection + * A class representing unordered, fixed sized collection * of objects. */ -public interface MOBYFixedCollection extends MOBYCollection +public class MOBYFixedCollection extends MOBYCollection { -} \ No newline at end of file + + public MOBYFixedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isResizable() { return false; } + public boolean isFixedSized() { return true; } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java 2004/07/29 23:33:59 1.2 @@ -1,14 +1,29 @@ package org.smoby.graph; +import java.util.*; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface representing collections that can be resized (i.e. + * A class representing collections that can be resized (i.e. * elements added to or removed from); such collections can be * either ordered or unordered. */ -public interface MOBYResizableCollection extends MOBYCollection +public abstract class MOBYResizableCollection extends MOBYCollection { + public MOBYResizableCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + /** * Return whether or not this collection is ordered. */ - public boolean isOrdered(); -} \ No newline at end of file + public abstract boolean isOrdered(); + + public boolean isResizable() { return true; } + public boolean isFixedSized() { return false; } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,23 @@ package org.smoby.graph; +import java.net.URI; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface to represent singular objects, i.e. those that are + * A class to represent singular objects, i.e. those that are * not collections. */ -public interface MOBYSingleElement extends MOBYGraphNode +public abstract class MOBYSingleElement extends MOBYGraphNode { -} + public MOBYSingleElement(Resource resource, Model underlying) + { + super(resource, underlying); + } + + public boolean isSingular() { return true; } + public boolean isCollection() { return false; } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,9 @@ package org.smoby.graph; -public interface MOBYPropertyValueConstraint +public abstract class MOBYPropertyValueConstraint { - public void validatePropertyValue(MOBYPropertyValueStatement stmt, - MOBYPropertyValue newValue) + public abstract void validatePropertyValue( + MOBYPropertyValueStatement stmt, + MOBYPropertyValue newValue) throws MOBYPropertyValueException; } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java 2004/07/29 23:33:59 1.2 @@ -1,28 +1,76 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYPropertyValueStatement +public class MOBYPropertyValueStatement extends MOBYDescriptor { + private Statement jenaStatement; + private MOBYPropertyValue currentValue; + private MOBYPropertyValueConstraint constraint; + + public MOBYPropertyValueStatement(Statement jenaStatement, + Model underlying) { + super(null, underlying); + this.jenaStatement = jenaStatement; + if (jenaStatement.getObject().canAs(Resource.class)) { + Resource value = (Resource) jenaStatement.getObject(); + currentValue = new MOBYResource(value); + } else { + Literal value = (Literal) jenaStatement.getObject(); + currentValue = new MOBYLiteral(value.getString()); + } + } + /** * Return the name of this property */ - public String getPropertyName(); + public String getPropertyName() { + return jenaStatement.getPredicate().getURI(); + } + public String toString() { + return jenaStatement.toString(); + } + /** * Return the value currently associated with this property */ - public MOBYPropertyValue getValue(); - + public MOBYPropertyValue getValue() { + return currentValue; + } + /** * Set the property value. This is just a placeholder; values of * different property types will be set to different types of * values. */ public void setPropertyValue(MOBYPropertyValue newValue) - throws MOBYPropertyValueException; - + throws MOBYPropertyValueException + { + if (constraint != null) { + constraint.validatePropertyValue(this, newValue); + } + + if (newValue.isLiteral()) { + MOBYLiteral literal = (MOBYLiteral) newValue; + jenaStatement.changeObject(literal.getStringValue()); + } else { + MOBYResource resource = (MOBYResource) newValue; + if (resource.isBlank()) { + jenaStatement.changeObject( + jenaStatement.getModel().createResource()); + } else { + jenaStatement.changeObject( + jenaStatement.getModel().createResource( + resource.getResourceURI())); + } + } + } + /** * Set the given constraint for this property value statement */ - public void setConstraint(MOBYPropertyValueConstraint constraint); -} \ No newline at end of file + public void setConstraint(MOBYPropertyValueConstraint constraint) { + this.constraint = constraint; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java 2004/07/29 23:33:59 1.2 @@ -1,10 +1,19 @@ package org.smoby.graph; +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface representing a resizable collection of objects, in + * A class representing a resizable collection of objects, in * which the order of the elements is not defined; the intention is * for the elements to represent possible choices for a value. */ -public interface MOBYEnumeration extends MOBYUnorderedCollection +public class MOBYEnumeration extends MOBYUnorderedCollection { -} + public MOBYEnumeration(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isEnumeration() { return true; } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java 2004/07/29 23:33:59 1.2 @@ -1,38 +1,84 @@ package org.smoby.graph; import java.io.*; +import com.hp.hpl.jena.rdf.model.*; /** - * The Provider interface represents a resource that provides a + * The Provider class represents a resource that provides a * service in MOBY. */ -public interface MOBYProvider extends MOBYDocument +public class MOBYProvider extends MOBYDocument { + private String name; + private String oneLineDescription; + private String moreInfoURI; + private MOBYUnorderedCollection operatesOn; + + public MOBYProvider(Resource resource, String name, String oneLineDescription, + String moreInfoURI, MOBYUnorderedCollection operatesOn, + Model underlying) + { + super(resource, underlying); + this.name = name; + this.oneLineDescription = oneLineDescription; + this.moreInfoURI = moreInfoURI; + this.operatesOn = operatesOn; + } + /** * Return a descriptive name for the provider. */ - public String getName(); - + public String getName() + { + return name; + } + /** * Return a short (one line) description for the provider. */ - public String getOneLineDescription(); - + public String getOneLineDescription() + { + return oneLineDescription; + } + /** * Return a URI that can be accessed to obtain more information * about the provider. */ - public String getMoreInfoURI(); + public String getMoreInfoURI() + { + return moreInfoURI; + } /** * Return a collection of graph nodes that this provider operates on. * Each graph node represents either a Graph or GraphCollection. */ - public MOBYUnorderedCollection getOperatesOn(); + public MOBYUnorderedCollection getOperatesOn() + { + return operatesOn; + } + public String toString() + { + StringBuffer sb = new StringBuffer(); + sb.append("Provider [name=\""); + sb.append(name); + sb.append("\", oneLineDescription=\""); + sb.append(oneLineDescription); + sb.append("\", moreInfoURI="); + sb.append(moreInfoURI); + sb.append("\"]"); + + return sb.toString(); + } + /** - * Provider implementations should be capable of serializing themselves + * Providers should be capable of serializing themselves * to an output stream */ - public void serialize(OutputStream out); -} \ No newline at end of file + public void serialize(OutputStream out) + { + underlying.write(out); + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java 2004/07/29 23:33:59 1.2 @@ -1,18 +1,22 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.Model; + /** - * A superinterface for things that can appear as the subject + * A superclass for things that can appear as the subject * or object of a statement. */ -public interface MOBYPropertyValue +public abstract class MOBYPropertyValue { /** - * Return whether or not this property value represents a literal + * Return whether or not this property value represents + * a literal value */ - public boolean isLiteral(); - + public abstract boolean isLiteral(); + /** - * Return whether or not this property value represents a resource + * Return whether or not this property value represents + * a resource */ - public boolean isResource(); + public abstract boolean isResource(); } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,14 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents a collection of RDF statements to be + * This class represents a collection of RDF statements to be * incorporated into the S-MOBY metadata repository. */ -public interface MOBYOntology extends MOBYDocument +public class MOBYOntology extends MOBYDocument { -} + public MOBYOntology(Resource resource, Model underlying) { + super(resource, underlying); + } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java 2004/06/18 21:37:52 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java 2004/07/29 23:33:59 1.2 @@ -1,25 +1,56 @@ package org.smoby.graph; import java.io.*; +import java.util.*; +import org.smoby.tools.*; +import com.hp.hpl.jena.rdf.model.*; /** - * An interface to represent a set of providers + * An class to represent a set of providers */ -public interface MOBYProviderSet extends MOBYDocument +public class MOBYProviderSet extends MOBYDocument { + private List providers = new ArrayList(); + + public MOBYProviderSet() + { + super(null, null); + } + /** - * Add a provider to the set + * Return the size of the set */ - public void addProvider(MOBYProvider provider); - + public int size() + { + return providers.size(); + } + /** - * Return the size of the set + * Add a provider to the set */ - public int size(); - + public void addProvider(MOBYProvider provider) + { + providers.add(provider); + } + /** * Provider sets should be capable of serializing themselves * to an output stream */ - public void serialize(OutputStream out); + public void serialize(OutputStream out) + { + Model merged = ModelFactory.createDefaultModel(); + + for (Iterator it = providers.iterator(); it.hasNext();) + { + MOBYProvider provider = (MOBYProvider) it.next(); + Model underlying = provider.getUnderlying(); + merged.add(underlying); + merged.setNsPrefixes(underlying.getNsPrefixMap()); + } + + Util.removeUnusedNsPrefixes(merged); + + merged.write(out); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java 2004/07/29 23:33:59 1.2 @@ -1,17 +1,36 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYMappingElement extends MOBYSingleElement + +public class MOBYMappingElement extends MOBYSingleElement { + private MOBYFixedCollection statements; + private MOBYCollection nestedElements; + + public MOBYMappingElement(Resource resource, MOBYFixedCollection statements, + MOBYCollection nestedElements, Model underlying) + { + super(resource, underlying); + this.statements = statements; + this.nestedElements = nestedElements; + } + /** * Return the collection of property-setting statements associated - * with this subject. + * with this mapping element. */ - public MOBYFixedCollection getPropertyValueStatements(); - + public MOBYFixedCollection getPropertyValueStatements() + { + return statements; + } + /** - * Return the collection of mappings that are nested within this subject - * through its role as a data structure. + * Return the collection of mappings that are nested within this + * mapping element through its role as a data structure. */ - public MOBYCollection getNestedElements(); + public MOBYCollection getNestedElements() { + return nestedElements; + } + } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/19 18:21:36 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/29 23:33:59 1.3 @@ -1,17 +1,43 @@ package org.smoby.graph; -import java.net.URI; - -import com.hp.hpl.jena.rdf.model.Resource; +import com.hp.hpl.jena.rdf.model.*; /** - * The Resource interface represents things that are available + * The MOBYDescriptor class represents things that are available * at a URI. */ -public interface MOBYDescriptor +public abstract class MOBYDescriptor { + protected Model underlying; + protected Resource resource; + + public MOBYDescriptor(Resource resource, Model underlying) + { + this.resource = resource; + this.underlying = underlying; + } + + /** + * Return the resource associated with this descriptor. + */ + public Resource getResource() + { + return resource; + } + + /** + * Return the underlying Jena model + */ + public Model getUnderlying() + { + return underlying; + } + /** - * Return the URI represented by this node. + * Return the URI of the underlying resource, if any. */ - public Resource getResource(); -} + public String getURI() + { + return (resource == null) ? null : resource.getURI(); + } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,13 +1,22 @@ package org.smoby.graph; -/** - * An interface representing resizable collection of objects, in - * which the order of the elements is defined. - */ -public interface MOBYOrderedCollection extends MOBYResizableCollection +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + +public class MOBYOrderedCollection extends MOBYResizableCollection { + public MOBYOrderedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isOrdered() { return true; } + /** * Return the object at a given zero-based index. */ - public Object get(int index); + public Object get(int index) + { + return elements.get(index); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java 2004/07/29 23:33:59 1.2 @@ -1,30 +1,50 @@ package org.smoby.graph; -import java.util.Iterator; +import com.hp.hpl.jena.rdf.model.*; +import java.util.*; /** - * A common interface for collections, both fixed sized and resizeable, of - * elements in MOBY graphs. + * A common abstract class for collections, both fixed sized and resizeable, + * of elements in MOBY graphs. */ -public interface MOBYCollection extends MOBYGraphNode +public abstract class MOBYCollection extends MOBYGraphNode { + protected List elements = new ArrayList(); + + public MOBYCollection(Resource resource, List elements, Model underlying) + { + super(resource, underlying); + for (Iterator it = elements.iterator(); it.hasNext();) { + this.elements.add(it.next()); + } + } + /** - * Return whether or not the collection is fixed in size + * Return the size of the collection. */ - public boolean isFixedSized(); - + public int size() + { + return elements.size(); + } + /** - * Return whether or not the collection is resizable + * Return an iterator for traversing the elements */ - public boolean isResizable(); + public Iterator iterator() + { + return elements.iterator(); + } /** - * Return an iterator for traversing the elements + * Return whether or not the collection is fixed in size */ - public Iterator iterator(); + public abstract boolean isFixedSized(); /** - * Return the size of the collection. + * Return whether or not the collection is resizable */ - public int size(); + public abstract boolean isResizable(); + + public boolean isSingular() { return false; } + public boolean isCollection() { return true; } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,14 +1,28 @@ package org.smoby.graph; +import java.util.*; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface representing resizable collection of objects, in + * A class representing resizable collection of objects, in * which the order of the elements is not defined. */ -public interface MOBYUnorderedCollection extends MOBYResizableCollection +public class MOBYUnorderedCollection extends MOBYResizableCollection { + public MOBYUnorderedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isOrdered() { return false; } + /** * Return whether or not the elements of this collection represent * choices (i.e. elements of an enumeration of possible values). */ - public boolean isEnumeration(); + public boolean isEnumeration() { return false; } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java 2004/07/29 23:33:59 1.2 @@ -1,13 +1,26 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents singular (i.e. not collection) subgraphs + * This class represents singular (i.e. not collection) subgraphs * that have a single mapping. */ -public interface MOBYGraph extends MOBYSingleElement +public class MOBYGraph extends MOBYSingleElement { + private MOBYGraphNode hasMapping; + + public MOBYGraph(Resource resource, MOBYGraphNode hasMapping, Model underlying) + { + super(resource, underlying); + this.hasMapping = hasMapping; + } + /** * Return the object of this graph's hasMapping property. */ - public MOBYGraphNode gethasMapping(); + public MOBYGraphNode getHasMapping() + { + return hasMapping; + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java 2004/07/29 23:33:59 1.2 @@ -1,23 +1,33 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface for nodes in an RDF graph; these nodes are either + * An abstract class for nodes in an RDF graph; these nodes are either * collections or singular elements. */ -public interface MOBYGraphNode extends MOBYDescriptor +public abstract class MOBYGraphNode extends MOBYDescriptor { + public MOBYGraphNode(Resource resource, Model underlying) + { + super(resource, underlying); + } + /** * Return whether or not this node represents a blank node */ - public boolean isBlank(); + public boolean isBlank() + { + return (resource == null) || (resource.getURI() == null); + } /** * Return whether or not this object is a collection. */ - public boolean isCollection(); + public abstract boolean isCollection(); /** * Return whether or not this object is a singular element. */ - public boolean isSingular(); + public abstract boolean isSingular(); } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,15 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** * An object that represents the object of a mapping. */ -public interface MOBYObject extends MOBYMappingElement +public class MOBYObject extends MOBYMappingElement { -} \ No newline at end of file + public MOBYObject(Resource resource, MOBYFixedCollection statements, + MOBYCollection nestedElements, Model underlying) + { + super(resource, statements, nestedElements, underlying); + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java 2004/07/29 23:33:59 1.2 @@ -1,6 +1,9 @@ package org.smoby.graph; -import java.net.URI; +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; /** * An object that represents the subject of one or more mappings. In @@ -16,11 +19,27 @@ * of which can itself be either a moby:Subject, an RDF data structure, * or both. This collection of elements is returned by getNestedMappings(). */ -public interface MOBYSubject extends MOBYMappingElement +public class MOBYSubject extends MOBYMappingElement { + /** + * The collection of direct mappings, i.e. moby:mapsTo statements + * whose subject is this. + */ + private MOBYUnorderedCollection directMappings; + + public MOBYSubject(Resource resource, MOBYFixedCollection statements, + MOBYUnorderedCollection directMappings, + MOBYCollection nestedMappings, Model underlying) + { + super(resource, statements, nestedMappings, underlying); + this.directMappings = directMappings; + } + /** * Return a resizable, unordered collection of the MOBYNode instances, * which are objects of mapsTo statements, whose subjects are this. */ - public MOBYUnorderedCollection getDirectMappings(); -} \ No newline at end of file + public MOBYUnorderedCollection getDirectMappings() { + return directMappings; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java 2004/07/29 23:33:59 1.2 @@ -1,6 +1,5 @@ package org.smoby.graph; - public class MOBYPropertyValueException extends Exception { public MOBYPropertyValueException(String message) { From mwilkinson at pub.open-bio.org Thu Jul 29 19:34:06 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 19:13:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNY6mG020893@pub.open-bio.org> mwilkinson Thu Jul 29 19:34:06 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv20855/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: okay,now it works properly. A new parameter RDF is returned in the Registration XML. This holds the RDF signature of your service. moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 21:53:54 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 23:34:06 1.7 @@ -30,11 +30,11 @@ sub serialize { - my ($model) = @_; + my ($self) = @_; my $xml = ''; my $serializer = new RDF::Core::Model::Serializer( - Model=>$model, + Model=>$self->model, Output=>\$xml, getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! ); From mwilkinson at pub.open-bio.org Thu Jul 29 19:34:06 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 19:13:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNY6n7020874@pub.open-bio.org> mwilkinson Thu Jul 29 19:34:06 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv20855/MOBY Modified Files: Central.pm Log Message: okay,now it works properly. A new parameter RDF is returned in the Registration XML. This holds the RDF signature of your service. moby-live/Perl/MOBY Central.pm,1.134,1.135 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.134 retrieving revision 1.135 diff -u -r1.134 -r1.135 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 21:53:53 1.134 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 23:34:06 1.135 @@ -1167,24 +1167,19 @@ # this is roundabout, I agree, but it is the most re-usable way to go at # the moment. - my ($si, $reg) = &findService(qw{ + my ($si, $reg) = &findService('',' $AuthURI; $serviceName; - "}); + '); unless ($si){ $SVC->DELETE_THYSELF; return &_error("Registration Failed - newly registered service could not be discovered",""); } - my $service = shift @{$si}; - unless ($service){ - $SVC->DELETE_THYSELF; - return &_error("Registration Failed - newly registered service could not be discovered",""); - } - - my $services = MOBY::Client::Central::_parseServices('', '', $service); + use MOBY::Client::Central; + my $services = MOBY::Client::Central::_parseServices('', '', $si); my $service_instance = shift @{$services}; my $storage = new RDF::Core::Storage::Memory; my $model = new RDF::Core::Model (Storage => $storage); @@ -1670,7 +1665,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if (scalar @{$findme{keywords}}){ + if ($findme{keywords} && (scalar @{$findme{keywords}})){ ++$criterion_count; $debug && _LOG("Keywords added; criterion count is now $criterion_count\n"); my $searchstring; @@ -1694,7 +1689,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if (scalar @{$findme{inputObjects}}){ + if ($findme{inputObjects} && (scalar @{$findme{inputObjects}})){ ++$criterion_count; $debug && _LOG("inputObject added; criterion count is now $criterion_count\n"); my $obj = (shift @{$findme{inputObjects}}); @@ -1727,7 +1722,7 @@ ++$valid_service_ids{$_}; } } - if (scalar @{$findme{outputObjects}}){ + if ($findme{outputObjects} && (scalar @{$findme{outputObjects}})){ ++$criterion_count; $debug && _LOG("outputObject added; criterion count is now $criterion_count\n"); my $obj = (shift @{$findme{outputObjects}}); From gss at pub.open-bio.org Thu Jul 29 19:34:44 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:14:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNYi6a020925@pub.open-bio.org> gss Thu Jul 29 19:34:43 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools In directory pub.open-bio.org:/tmp/cvs-serv20901/src/org/smoby/graph/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools added to the repository moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 19:34:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:14:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNYks3020959@pub.open-bio.org> gss Thu Jul 29 19:34:45 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools In directory pub.open-bio.org:/tmp/cvs-serv20938/src/org/smoby/graph/tools Added Files: MOBYProviderTraversalException.java MOBYProviderXMLGenerator.java MOBYProviderVisitor.java MOBYProviderTraverser.java Log Message: Visitor pattern for MOBY graphs, with example moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools MOBYProviderTraversalException.java,NONE,1.1 MOBYProviderXMLGenerator.java,NONE,1.1 MOBYProviderVisitor.java,NONE,1.1 MOBYProviderTraverser.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 29 19:35:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:14:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292335.i6TNZ9Ta020991@pub.open-bio.org> gss Thu Jul 29 19:35:09 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv20966/src/org/smoby/parser Modified Files: Parser.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/19 18:21:36 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/29 23:35:09 1.7 @@ -4,7 +4,6 @@ import java.net.*; import java.util.*; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.parser.*; import org.smoby.tools.ModelRetriever; import org.smoby.tools.Util; @@ -179,7 +178,7 @@ // Create and return an unordered collection of the parsed providers // - return MOBYObjectFactory.newUnorderedCollection(null, providers, null); + return new MOBYUnorderedCollection(null, providers, null); } /** @@ -211,9 +210,9 @@ // Create and return a new Provider object using the provider URI, name, // oneLineDescription, aboutURI, and collection of operatesOn subgraphs // - return MOBYObjectFactory.newProvider( + return new MOBYProvider( provider, name, oneLiner, aboutURI, - MOBYObjectFactory.newUnorderedCollection(provider, operatesOn, model), + new MOBYUnorderedCollection(provider, operatesOn, model), model); } @@ -234,7 +233,7 @@ // hasMapping property that leads to its mapping subgraph. // Resource hasMapping = getResourcePropertyValue(res, MOBY.hasMapping); - return MOBYObjectFactory.newGraph(res, parseHasMapping(hasMapping), model); + return new MOBYGraph(res, parseHasMapping(hasMapping), model); } else { @@ -318,9 +317,9 @@ // Create and return a Subject to describe this hasMapping subgraph // - return MOBYObjectFactory.newSubject(res, - MOBYObjectFactory.newFixedCollection(res, statements, model), - MOBYObjectFactory.newUnorderedCollection(res, directMappings, model), + return new MOBYSubject(res, + new MOBYFixedCollection(res, statements, model), + new MOBYUnorderedCollection(res, directMappings, model), collectionFor(res, nestedMappings), model); } @@ -362,8 +361,8 @@ // Create and return a new MOBYObject // Model model = res.getModel(); - return MOBYObjectFactory.newObject(res, - MOBYObjectFactory.newFixedCollection(res, statements, model), + return new MOBYObject(res, + new MOBYFixedCollection(res, statements, model), collectionFor(res, nested), model); } @@ -395,7 +394,7 @@ if (isMobyProperty(p, model)) { MOBYPropertyValueStatement pvalStmt = - MOBYObjectFactory.newPropertyValueStatement(stmt, model); + new MOBYPropertyValueStatement(stmt, model); Statement s = p.getProperty(RDFS.range); @@ -403,15 +402,15 @@ { Resource range = (Resource) s.getObject(); if (range.equals(XSD.date)) { - pvalStmt.setConstraint(MOBYObjectFactory.newDateConstraint()); + pvalStmt.setConstraint(new MOBYDateConstraint()); } else if (range.equals(XSD.integer)) { - pvalStmt.setConstraint(MOBYObjectFactory.newIntegerConstraint()); + pvalStmt.setConstraint(new MOBYIntegerConstraint()); } else if (range.equals(XSD.nonNegativeInteger)) { pvalStmt.setConstraint( - MOBYObjectFactory.newNonNegativeIntegerConstraint()); + new MOBYNonNegativeIntegerConstraint()); } else if (range.equals(XSD.nonPositiveInteger)) { pvalStmt.setConstraint( - MOBYObjectFactory.newNonPositiveIntegerConstraint()); + new MOBYNonPositiveIntegerConstraint()); } } @@ -486,13 +485,13 @@ private MOBYCollection collectionFor(Resource res, List elements) { if (isList(res)) { - return MOBYObjectFactory.newFixedCollection(res, elements, res.getModel()); + return new MOBYFixedCollection(res, elements, res.getModel()); } else if (isBag(res)) { - return MOBYObjectFactory.newUnorderedCollection(res, elements, res.getModel()); + return new MOBYUnorderedCollection(res, elements, res.getModel()); } else if (isSeq(res)) { - return MOBYObjectFactory.newOrderedCollection(res, elements, res.getModel()); + return new MOBYOrderedCollection(res, elements, res.getModel()); } else if (isAlt(res)) { - return MOBYObjectFactory.newEnumeration(res, elements, res.getModel()); + return new MOBYEnumeration(res, elements, res.getModel()); } else { return null; } From gss at pub.open-bio.org Thu Jul 29 19:37:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:17:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292337.i6TNbxZw021051@pub.open-bio.org> gss Thu Jul 29 19:37:59 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21026/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools DiscoveryQuery.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/15 20:27:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/29 23:37:59 1.2 @@ -8,7 +8,6 @@ import org.smoby.ref.tools.db.*; import org.smoby.tools.Util; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.vocabulary.*; import com.hp.hpl.jena.db.*; @@ -111,7 +110,7 @@ Model dbModel = null; try { - Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying(); + Model queryModel = ((MOBYProvider) queryProvider).getUnderlying(); String queryString = buildQueryString(queryModel); StorageManager manager = new StorageManager(); dbModel = manager.openDBModel(); @@ -129,7 +128,7 @@ } results.close(); - MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet(); + MOBYProviderSet returnSet = new MOBYProviderSet(); for (Iterator it = matching.iterator(); it.hasNext();) { From gss at pub.open-bio.org Thu Jul 29 19:38:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:18:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292338.i6TNce9x021089@pub.open-bio.org> gss Thu Jul 29 19:38:40 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv21064/src/org/smoby/ref/servlets/example Modified Files: HelloWorldServlet.java Log Message: Remove use of MOBYObjectFactory moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/21 22:01:19 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/29 23:38:40 1.3 @@ -6,7 +6,6 @@ import javax.servlet.http.*; import org.smoby.graph.*; -import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.ref.servlets.*; import org.smoby.servlet.*; @@ -34,7 +33,7 @@ MOBYGraph graph = (MOBYGraph) provider.getOperatesOn().iterator().next(); - MOBYSubject subject = (MOBYSubject) graph.gethasMapping(); + MOBYSubject subject = (MOBYSubject) graph.getHasMapping(); MOBYObject object = (MOBYObject) subject.getDirectMappings().iterator().next(); @@ -43,7 +42,7 @@ object.getPropertyValueStatements().iterator().next(); stmt.setPropertyValue( - MOBYObjectFactory.newLiteralValue("Hello, world!")); + new MOBYLiteral("Hello, world!")); } // Silently ignore graphs without the required form From gss at pub.open-bio.org Thu Jul 29 19:38:53 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:18:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292338.i6TNcr5E021119@pub.open-bio.org> gss Thu Jul 29 19:38:53 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21094/src/org/smoby/ref/tools Modified Files: KeywordFinder.java Log Message: Remove use of MOBYObjectFactory moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools KeywordFinder.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java 2004/07/21 22:01:19 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java 2004/07/29 23:38:53 1.2 @@ -85,7 +85,7 @@ if (node instanceof MOBYGraph) { MOBYGraph graph = (MOBYGraph) node; - addSubjectKeywordsFor(graph.gethasMapping()); + addSubjectKeywordsFor(graph.getHasMapping()); } else if (node instanceof MOBYCollection) { From gss at pub.open-bio.org Thu Jul 29 19:39:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:18:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292339.i6TNdH12021149@pub.open-bio.org> gss Thu Jul 29 19:39:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv21124/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageManager.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/29 23:39:17 1.3 @@ -1,7 +1,6 @@ package org.smoby.ref.tools.db; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.ref.tools.*; import org.smoby.tools.Util; import org.smoby.vocabulary.*; @@ -60,7 +59,7 @@ public void registerProvider(MOBYProvider provider, Date lastModifiedDate) throws StorageException { - Model model = ((MOBYProviderImpl) provider).getUnderlying(); + Model model = ((MOBYProvider) provider).getUnderlying(); Model dbModel = null; String uriString = provider.getResource().getURI(); Resource uri = model.createResource(uriString); From gss at pub.open-bio.org Thu Jul 29 19:44:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:24:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNiaFR021283@pub.open-bio.org> gss Thu Jul 29 19:44:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc In directory pub.open-bio.org:/tmp/cvs-serv21259/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 19:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:24:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicbn021313@pub.open-bio.org> gss Thu Jul 29 19:44:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/15 20:30:18 1.11 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/29 23:44:37 1.12 @@ -6,7 +6,6 @@ import javax.servlet.http.*; import org.smoby.servlet.*; import org.smoby.graph.*; -import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.vocabulary.*; import com.acmepubs.vocabulary.*; @@ -54,7 +53,7 @@ // The subject of the graph should be a MOBYSubject // - MOBYSubject subject = (MOBYSubject) graph.gethasMapping(); + MOBYSubject subject = (MOBYSubject) graph.getHasMapping(); // That object should have a single subproperty of moby:Property, // namely geneSymbol; its value should be a literal @@ -77,8 +76,7 @@ // based on a base URI string and the geneSymbol that was passed // String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus="; - literal = MOBYObjectFactory.newLiteralValue( - baseURI + geneSymbol); + literal = new MOBYLiteral(baseURI + geneSymbol); stmt.setPropertyValue(literal); } } From gss at pub.open-bio.org Thu Jul 29 19:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:24:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNic60021333@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/server/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/06/18 21:42:34 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/29 23:44:38 1.7 @@ -111,7 +111,7 @@ Model dbModel = null; try { - Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying(); + Model queryModel = queryProvider.getUnderlying(); String queryString = buildQueryString(queryModel); StorageManager manager = new StorageManager(); dbModel = manager.openDBModel(); @@ -129,7 +129,7 @@ } results.close(); - MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet(); + MOBYProviderSet returnSet = new MOBYProviderSet(); for (Iterator it = matching.iterator(); it.hasNext();) { From gss at pub.open-bio.org Thu Jul 29 19:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:24:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicgw021373@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/06/18 21:42:34 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/29 23:44:38 1.6 @@ -58,7 +58,7 @@ public void registerProvider(MOBYProvider provider, Date lastModifiedDate) throws StorageException { - Model model = ((MOBYProviderImpl) provider).getUnderlying(); + Model model = provider.getUnderlying(); Model dbModel = null; String uriString = provider.getURI(); Resource uri = model.createResource(uriString); From gss at pub.open-bio.org Thu Jul 29 19:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Jul 29 19:24:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicra021352@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients Modified Files: SimpleProviderEngagerPanel.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/15 20:20:37 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/29 23:44:38 1.3 @@ -120,7 +120,7 @@ } else { - String graphURI = provider.getURI(); + String graphURI = provider.getResource().getURI(); HTTPRequest request = HTTPRequest.newPostRequest(graphURI); request.addParameter("graph", graphString); HTTPResponse response = request.send(); From mwilkinson at pub.open-bio.org Thu Jul 29 20:07:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 19:46:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300007.i6U07IUv021549@pub.open-bio.org> mwilkinson Thu Jul 29 20:07:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv21507/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: the adaptor now writes to a new field in the database - signatureURL - which is where Nina's agent expects to find the RDF corresponding to the service. This can be null, if you want to temporarily register a service. moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/26 17:09:09 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:07:18 1.4 @@ -204,7 +204,7 @@ my ($self, %args) = @_; my $dbh = $self->dbh; - $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, + $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description, signatureURL) values (?,?,?,?,?,?,?,?,?)}, undef, $args{'category'}, $args{'servicename'}, @@ -213,7 +213,8 @@ $args{'url'}, $args{'contact_email'}, $args{'authoritative'}, - $args{'description'}); + $args{'description'}, + $args{'signatureURL'}); my $id = $dbh->{mysql_insertid}; return $id; From mwilkinson at pub.open-bio.org Thu Jul 29 20:07:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 19:46:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300007.i6U07IXA021530@pub.open-bio.org> mwilkinson Thu Jul 29 20:07:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv21507/MOBY Modified Files: Central.pm service_instance.pm Log Message: the adaptor now writes to a new field in the database - signatureURL - which is where Nina's agent expects to find the RDF corresponding to the service. This can be null, if you want to temporarily register a service. moby-live/Perl/MOBY Central.pm,1.135,1.136 service_instance.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.135 retrieving revision 1.136 diff -u -r1.135 -r1.136 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 23:34:06 1.135 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:07:18 1.136 @@ -1082,11 +1082,12 @@ sub registerService { my ($pkg, $payload) = @_; - my ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARY) = &_registerServicePayload($payload); + my ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARY, $signatureURL) = &_registerServicePayload($payload); $authoritativeService = defined($authoritativeService)?1:0; my $error; $error .="missing serviceName \n" unless defined $serviceName; $error .="missing serviceType \n" unless defined $serviceType; + $error .="missing signatureURL \n" unless defined $signatureURL; $error .="missing authURI \n" unless defined $AuthURI; $error .="missing contactEmail \n" unless defined $contactEmail; return &_error("Malformed authURI - must not have an http:// prefix","") if $AuthURI =~ '[/:]'; @@ -1141,6 +1142,7 @@ contact_email => $contactEmail, authoritative => $authoritativeService, description => $desc, + signatureURL => $signatureURL, ); return &_error("Service registration failed for unknown reasons","") if (!defined $SVC); @@ -1167,13 +1169,10 @@ # this is roundabout, I agree, but it is the most re-usable way to go at # the moment. - my ($si, $reg) = &findService('',' - - + my ($si, $reg) = &findService(''," $AuthURI; $serviceName; - - '); + "); unless ($si){ $SVC->DELETE_THYSELF; return &_error("Registration Failed - newly registered service could not be discovered",""); @@ -1356,13 +1355,15 @@ my $contactEmail = &_nodeTextContent($Object, "contactEmail"); my $authoritativeService = &_nodeTextContent($Object, "authoritativeService"); my $URL = &_nodeTextContent($Object, "URL"); + my $signatureURL = &_nodeTextContent($Object, "signatureURL"); my $desc = &_nodeTextContent($Object, "Description"); my $INPUTS = &_nodeRawContent($Object, "Input"); # returns array ref my $OUTPUTS = &_nodeRawContent($Object, "Output"); # returns array ref my $SECONDARIES = &_nodeRawContent($Object, "secondaryArticles"); # returns array ref - return ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARIES); + return ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARIES, $signatureURL); } + sub _extractObjectTypes { my ($DOM) = @_; # DOM is either a or a article $debug && &_LOG("\n\n\nExtracting object types from \n$DOM \n\n"); @@ -2878,7 +2879,7 @@ my $output=""; my $sth = $dbh->prepare(q{ select - category, url, servicename, service_type_uri, authority_id, description, authoritative, contact_email + category, url, servicename, service_type_uri, authority_id, description, authoritative, contact_email, signatureURL from service_instance where service_instance_id = ?}); my $sth_simple_in = $dbh->prepare("select object_type_uri, namespace_type_uris, article_name from simple_input where service_instance_id=? and collection_input_id IS NULL"); @@ -2896,8 +2897,9 @@ foreach (@ids){ $sth->execute($_); - my ($category, $url, $servicename, $service_type_uri, $authority_id, $desc, $authoritative, $email) = $sth->fetchrow_array; + my ($category, $url, $servicename, $service_type_uri, $authority_id, $desc, $authoritative, $email, $signatureURL) = $sth->fetchrow_array; #print "\n\nAFTER EXECUTE $category, $servicename, $service_type_uri, $authority_id, $desc, $authoritative\n\n"; + $signatureURL ||=""; next unless ($servicename && $authority_id); my $service_type = $OSserv->getServiceCommonName($service_type_uri); my ($authURI) = $dbh->selectrow_array(q{select authority_uri from authority where authority_id=?},undef,$authority_id); @@ -2907,6 +2909,7 @@ $output .= "\t$category\n"; $output .= "\t\n$desc\n\t\n"; $output .= "\t$email\n"; + $output .= "\t$signatureURL\n"; $output .= "\t$url\n"; $output .="\t\n"; $sth_simple_in->execute($_); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/09 00:21:53 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:07:18 1.7 @@ -66,6 +66,7 @@ service_type_uri => [undef, 'read/write'], authority => [undef, 'read/write'], authority_uri => [undef, 'read/write'], + signatureURL => [undef, 'read/write'], url => [undef, 'read/write'], inputs => [undef, 'read/write'], outputs => [undef, 'read/write'], @@ -128,6 +129,12 @@ (defined $val) && ($self->{url} = $val); return $self->{url} } + sub signatureURL{ + my ($self, $val) = @_; + if (defined $val && $self->signatureURL){return undef} + (defined $val) && ($self->{signatureURL} = $val); + return $self->{signatureURL} + } sub contact_email { my ($self, $val) = @_; if (defined $val && $self->contact_email){return undef} @@ -240,7 +247,10 @@ url => $self->url, contact_email => $self->contact_email, authoritative => $self->authoritative, - description => $self->description); + description => $self->description, + signatureURL => $self->signatureURL, + ); + $self->service_instance_id($id); $self->{__exists__} = 1; # this service now exists } else { # if it doesn't exist, and you havne't given me anyting I need to create it, then bail out From mwilkinson at pub.open-bio.org Thu Jul 29 20:14:15 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 19:53:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300014.i6U0EFkP021656@pub.open-bio.org> mwilkinson Thu Jul 29 20:14:15 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv21637/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: adding the new parameter into the test suite moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.19,1.20 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/12 00:39:37 1.19 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:14:15 1.20 @@ -159,6 +159,7 @@ serviceName => "myfirstservice", serviceType => "Retrieval", authURI => "www.illuminae.com", + signatureURL => "http://www.illuminae.com/somewhere", contactEmail => 'your@mail.address', description => "this is my first service", category => "moby", @@ -182,6 +183,7 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your@mail.address', + signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -198,6 +200,7 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your@mail.address', + signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", From mwilkinson at pub.open-bio.org Thu Jul 29 20:16:32 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 19:56:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300016.i6U0GWli021724@pub.open-bio.org> mwilkinson Thu Jul 29 20:16:32 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv21705/MOBY/Client Modified Files: Central.pm Log Message: adding the new parameter into the client library moby-live/Perl/MOBY/Client Central.pm,1.77,1.78 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.77 retrieving revision 1.78 diff -u -r1.77 -r1.78 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/29 21:53:54 1.77 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/30 00:16:32 1.78 @@ -706,6 +706,7 @@ my $email = $a{contactEmail}; $email ||=""; my $URL = $a{URL}; $URL ||=""; my $desc = $a{description}; $desc ||=""; + my $signatureURL = $a{signatureURL}; $signatureURL ||=""; my $Category = lc($a{category}); chomp $Category; $Category ||=""; return $self->errorRegXML("Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category") unless (($Category eq 'moby') || ($Category eq 'wsdl')); return $self->errorRegXML("All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary") unless ( @@ -717,6 +718,7 @@ $name $type + $signatureURL $URL $authURI $email"; From mwilkinson at pub.open-bio.org Thu Jul 29 20:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 20:19:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9Vi021885@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv21862/MOBY Modified Files: Central.pm service_instance.pm Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/MOBY Central.pm,1.136,1.137 service_instance.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.136 retrieving revision 1.137 diff -u -r1.136 -r1.137 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:07:18 1.136 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:40:09 1.137 @@ -1087,7 +1087,7 @@ my $error; $error .="missing serviceName \n" unless defined $serviceName; $error .="missing serviceType \n" unless defined $serviceType; - $error .="missing signatureURL \n" unless defined $signatureURL; +# $error .="missing signatureURL \n" unless defined $signatureURL; $error .="missing authURI \n" unless defined $AuthURI; $error .="missing contactEmail \n" unless defined $contactEmail; return &_error("Malformed authURI - must not have an http:// prefix","") if $AuthURI =~ '[/:]'; @@ -1431,9 +1431,12 @@ return &_error("The service specified by authority=$authURI servicename=$serviceName does not exist in the registry", "") unless (MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI, test => 1)); my $SERVICE = MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI); - my $result = $SERVICE->DELETE_THYSELF; - - if ($result){ + if ($SERVICE->signatureURL){ + return &_error("it is illegal to register a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); + } + + my $result = $SERVICE->DELETE_THYSELF; + if ($result){ return &_success("Service Deregistered Successfully",""); } else { return &_error("Service deletion failed for unknown reasons",""); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:07:18 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:40:09 1.8 @@ -231,6 +231,8 @@ $self->contact_email($existing_service->{'email'}); $self->description($existing_service->{'desc'}); $self->authority($existing_service->{'authURI'}); + $self->signatureURL($existing_service->{'signatureURL'}); + $self->{__exists__} = 1; # this service already existed } elsif (!($existing_service) # if it doesn't exist && (defined $self->category) # and you have given me things I need to create it From mwilkinson at pub.open-bio.org Thu Jul 29 20:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 20:19:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9gp021924@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv21862/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.20,1.21 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:14:15 1.20 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:40:09 1.21 @@ -1,7 +1,7 @@ #!/usr/bin/perl -w use MOBY::Client::Central; -my $v = 1 if ($ARGV[0] eq "verbose"); +my $v = 1 if ($ARGV[0] && ($ARGV[0] eq "verbose")); sub TEST { # test of Registration object ($reg, $test, $expect) = @_; From mwilkinson at pub.open-bio.org Thu Jul 29 20:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 20:19:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9qT021904@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv21862/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:07:18 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:40:09 1.5 @@ -169,7 +169,7 @@ my ($self, %args) = @_; my $dbh = $self->dbh; - my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? + my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc, $signatureURL) = $dbh->selectrow_array( # does this service already exist? q{select service_instance_id, category, @@ -179,7 +179,8 @@ url, service_instance.contact_email, authoritative, - description + description, + signatureURL from service_instance, authority where service_instance.authority_id = authority.authority_id From mwilkinson at pub.open-bio.org Thu Jul 29 21:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 20:54:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1EiwK022137@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv22099/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:40:09 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 01:14:44 1.6 @@ -193,6 +193,7 @@ name => $name, servcetype => $typeURI, authURI => $authURI, + signatureURL => $signatureURL, url => $url, email => $email, authoritative => $authoritative, From mwilkinson at pub.open-bio.org Thu Jul 29 21:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 20:54:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1Eium022118@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv22099/MOBY Modified Files: Central.pm Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/MOBY Central.pm,1.137,1.138 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.137 retrieving revision 1.138 diff -u -r1.137 -r1.138 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:40:09 1.137 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 01:14:44 1.138 @@ -1432,7 +1432,7 @@ return &_error("The service specified by authority=$authURI servicename=$serviceName does not exist in the registry", "") unless (MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI, test => 1)); my $SERVICE = MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI); if ($SERVICE->signatureURL){ - return &_error("it is illegal to register a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); + return &_error("it is illegal to deregister a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); } my $result = $SERVICE->DELETE_THYSELF; From mwilkinson at pub.open-bio.org Thu Jul 29 21:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Jul 29 20:54:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1EixZ022157@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv22099/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.21,1.22 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:40:09 1.21 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 01:14:44 1.22 @@ -159,7 +159,6 @@ serviceName => "myfirstservice", serviceType => "Retrieval", authURI => "www.illuminae.com", - signatureURL => "http://www.illuminae.com/somewhere", contactEmail => 'your@mail.address', description => "this is my first service", category => "moby", @@ -183,7 +182,6 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your@mail.address', - signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -200,7 +198,6 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your@mail.address', - signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -266,10 +263,14 @@ serviceName => "myfirstservice", authURI => "www.illuminae.com", ), 28, 1); - -TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 28, 1); -TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 29, 1); -TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 30, 1); +#TEST($C->deregisterService( +# serviceName => "getDragonSimpleAnnotatedImages", +# authURI => "www.illuminae.com", +# ), 29, 0); # cant deregister a service with a signatureURL + +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 30, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 31, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 32, 1); exit 0; From gordonp at pub.open-bio.org Wed Jul 7 12:02:48 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed, 7 Jul 2004 12:02:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071602.i67G2mnT032210@pub.open-bio.org> gordonp Wed Jul 7 12:02:47 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32166/shared Modified Files: MobyPrefixResolver.java Log Message: Fixed issues with SOAP payload parsing related to namespaces and encoding schemes, works with Axis 1.1beta without warnings too moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2004/07/07 16:02:47 1.2 @@ -21,9 +21,13 @@ public class MobyPrefixResolver implements PrefixResolver{ public static final String MOBY_XML_NAMESPACE = "http://www.biomoby.org/moby"; public static final String MOBY_XML_PREFIX = "moby"; + public static final String MOBY_TRANSPORT_NAMESPACE = "http://biomoby.org/"; + public static final String MOBY_TRANSPORT_PREFIX = "mobyt"; public static final String XSI_NAMESPACE1999 = "http://www.w3.org/1999/XMLSchema-instance"; public static final String XSI_NAMESPACE2001 = "http://www.w3.org/2001/XMLSchema-instance"; public static final String XSI_PREFIX = "xsi"; + public static final String XSI1999_PREFIX = "xsi1999"; + public static final String XSI2001_PREFIX = "xsi2001"; /** * We don't really implement this as it can be extremely complicated. @@ -57,8 +61,17 @@ else if(MOBY_XML_PREFIX.equals(prefix)){ return MOBY_XML_NAMESPACE; } + else if(MOBY_TRANSPORT_PREFIX.equals(prefix)){ + return MOBY_TRANSPORT_NAMESPACE; + } else if(XSI_PREFIX.equals(prefix)){ - return XSI_NAMESPACE1999; //Crappy Perl XML Schema namespace usage is out of date + return XSI_NAMESPACE1999; //Crappy Perl XML Schema namespace usage is out of date, use it by default + } + else if(XSI1999_PREFIX.equals(prefix)){ + return XSI_NAMESPACE1999; + } + else if(XSI2001_PREFIX.equals(prefix)){ + return XSI_NAMESPACE2001; //Used by Axis } else{ return ""; // Indicates that we don't have a mapping for this prefix From gordonp at pub.open-bio.org Wed Jul 7 12:02:48 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed, 7 Jul 2004 12:02:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071602.i67G2mxp032191@pub.open-bio.org> gordonp Wed Jul 7 12:02:47 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32166/client Modified Files: MobyRequest.java Log Message: Fixed issues with SOAP payload parsing related to namespaces and encoding schemes, works with Axis 1.1beta without warnings too moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/05/20 16:08:05 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/07/07 16:02:47 1.4 @@ -16,9 +16,7 @@ import javax.xml.parsers.ParserConfigurationException; import javax.xml.transform.TransformerException; import javax.xml.namespace.QName; -import org.w3c.dom.Document; -import org.w3c.dom.Node; -import org.w3c.dom.Element; +import org.w3c.dom.*; // Utilities import java.util.Hashtable; @@ -34,6 +32,7 @@ import org.w3c.dom.NodeList; import org.apache.axis.message.MessageElement; import java.io.PrintStream; +import java.io.StringBufferInputStream; /** * This class handles the WSDL transaction to request a response @@ -56,6 +55,7 @@ protected MobyDataSecondaryInstance[] secondaryData = null; protected Vector outputData = null; protected Central mobyCentral = null; + protected PrefixResolver mobyPrefixResolver = null; protected Hashtable wsdlCache = null; protected String lastWsdlCacheKey = null; @@ -69,6 +69,7 @@ protected XPathContext xpath_context; protected String responseString = null; + private XPath stringEncodedXPath; private XPath base64EncodedXPath; private XPath queryResponseXPath; private XPath simpleChildXPath; @@ -97,11 +98,20 @@ } xpath_context = new XPathContext(); - PrefixResolver mobyPrefixResolver = new MobyPrefixResolver(); + mobyPrefixResolver = new MobyPrefixResolver(); // Now compile the XPath statements that will be used fetch data from the server response try{ - base64EncodedXPath = new XPath("//*[@xsi:type=\"SOAP-ENC:base64\"]", null, mobyPrefixResolver, XPath.SELECT); + base64EncodedXPath = new XPath("//*[starts-with(substring-after(@"+ + MobyPrefixResolver.XSI1999_PREFIX+ + ":type, ':'), \"base64\") or starts-with(substring-after(@"+ + MobyPrefixResolver.XSI2001_PREFIX+ + ":type, ':'), \"base64\")]", null, mobyPrefixResolver, XPath.SELECT); + stringEncodedXPath = new XPath("//*[substring-after(@"+ + MobyPrefixResolver.XSI1999_PREFIX+ + ":type, ':')=\"string\" or substring-after(@"+ + MobyPrefixResolver.XSI2001_PREFIX+ + ":type, ':')=\"string\"]", null, mobyPrefixResolver, XPath.SELECT); queryResponseXPath = new XPath("//moby:mobyData | //mobyData", null, mobyPrefixResolver, XPath.SELECT); simpleChildXPath = new XPath("moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT); collectionChildXPath = new XPath("moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT); @@ -306,23 +316,25 @@ // Should initialize endpoint, etc. This call is AXIS SPECIFIC, otherwise you'll // have to do the call's info setting manually. //((org.apache.axis.client.Call) soapCall).setSOAPService(soapService); - soapCall.setPortTypeName(new QName("http://biomoby.org/", - mobyService.getName() + "PortType")); - soapCall.setOperationName(new QName("http://biomoby.org/", - mobyService.getName())); + soapCall.removeAllParameters(); soapCall.setTargetEndpointAddress(mobyService.getURL()); + soapCall.setPortName(new QName("http://biomoby.org/", + mobyService.getName() + "PortType")); + //soapCall.setOperationName(new QName("http://biomoby.org/", + // mobyService.getName())); soapCall.setSOAPActionURI("http://biomoby.org/#" + mobyService.getName()); - soapCall.setReturnType(XMLType.SOAP_STRING); - soapCall.removeAllParameters(); MobyData[] requiredInputData = mobyService.getPrimaryInputs(); if(requiredInputData == null) return; // A method requiring no input? else{ // There is one argument, the MOBY request object string - soapCall.addParameter("MOBYRequest", - XMLType.SOAP_STRING, - stringType, - ParameterMode.IN); + /*soapCall.setReturnType(new QName("http://biomoby.org/", mobyService.getName())); + soapCall.addParameter("MOBYRequest", + XMLType.SOAP_STRING, + stringType, + ParameterMode.IN);*/ + if(debug) + debugPS.println("Set returnType after addParameter was " + soapCall.getReturnType()); } return; } @@ -337,9 +349,12 @@ //Setup mobyXMLInputData[0] = mobyInputXML; + if(debug) + debugPS.println("returnType just before invoke call is " + soapCall.getReturnType()); Object returnedObject = null; try{ - returnedObject = soapCall.invoke(mobyXMLInputData); + returnedObject = soapCall.invoke(new QName("http://biomoby.org/", + mobyService.getName()), mobyXMLInputData); } catch(Exception e){ throw new SOAPException("While invoking SOAP Call: " + e); @@ -354,6 +369,7 @@ return decodeSOAPMessage(resultDom); //return resultDom; } catch(Exception e){ + e.printStackTrace(); throw new SOAPException("Could not get SOAP response as DOM Element: "+ e); } @@ -368,53 +384,143 @@ * @return The root element of the MOBY response DOM */ protected Element decodeSOAPMessage(Element n) throws SOAPException, MobyException{ - if(n == null){ throw new SOAPException("SOAP Message given to decode is null"); } - // Find base64 encoded elements in the SOAP message using XPath NodeList node_list = null; + Node responseNode = null; + XPath responseElementXPath = null; try{ - node_list = runXPath(base64EncodedXPath, n); + responseElementXPath = new XPath("//"+ MobyPrefixResolver.MOBY_TRANSPORT_PREFIX+ + ":"+mobyService.getName()+"Response", + null, mobyPrefixResolver, XPath.SELECT); }catch(TransformerException te){ throw new SOAPException("Cannot select SOAP nodes due to exception "+ + "while compiling XPath statement (code bug?):" +te); + } + try{ + node_list = runXPath(responseElementXPath, n); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select SOAP nodes due to exception "+ "while executing XPath statement:" +te); } if(node_list == null || node_list.getLength() == 0){ - // Note: before giving up we should really have a plain string check as per the MOBY API 0.6 - throw new SOAPException("Could not find a Base64 encoded SOAP payload"); + throw new SOAPException("Could not find a response element in SOAP payload"); } - // Do decoding for each part found - for(int i = 0; i < node_list.getLength(); i++){ - + + if(node_list.getLength() > 1){ + throw new SOAPException("Found more than one response element in SOAP payload, " + + "unable to resolve ambiguity of the payload (service provider error?)"); + } + responseNode = node_list.item(0); + + // Find base64 encoded elements in the SOAP message using XPath and + // replace them with the real decoded contents + node_list = null; + try{ + node_list = runXPath(base64EncodedXPath, responseNode); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select base64 encoded SOAP nodes due to exception "+ + "while executing XPath statement:" +te); + } + if(debug && node_list != null){ + debugPS.println("There were " + node_list.getLength() + + " base64 encoded elements in the data"); + } + + // Do decoding for each base64 part found + for(int i = 0; node_list != null && i < node_list.getLength(); i++){ org.w3c.dom.Node change = node_list.item(i); - change.normalize(); + /* Make sure the text data is all put into one contiguous piece for decoding*/ + change.normalize(); + byte[] decodedBytes = org.apache.axis.encoding.Base64.decode(change.getFirstChild().getNodeValue()); String newText = new String(decodedBytes); if(debug){ debugPS.println("New decoded text is" + newText); } - // release resources related to the Xpath execution, since we won't be using this doc anymore - releaseXPath(n); - - responseString = new String(decodedBytes); - // Parse the MOBY XML document payload - Document domDoc = null; - try{ - domDoc = docBuilder.parse(new ByteArrayInputStream(decodedBytes)); - } catch(org.xml.sax.SAXException saxe){ - throw new MobyException("The SOAP payload defining the MOBY Result " + - "could not be parsed: " + saxe); - } catch(java.io.IOException ioe){ - throw new MobyException("The SOAP payload defining the MOBY Result " + - " could not be read (from a String!)" + ioe); + // Swap out this node for the decoded data + change.getParentNode().replaceChild(n.getOwnerDocument().createTextNode(new String(decodedBytes)), + change); + } + + // Now see if there are any strings that need decoding + node_list = null; + try{ + node_list = runXPath(stringEncodedXPath, responseNode); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select base64 encoded SOAP nodes due to exception "+ + "while executing XPath statement:" +te); + } + + // Do decoding for each base64 part found + for(int i = 0; node_list != null && i < node_list.getLength(); i++){ + org.w3c.dom.Node change = node_list.item(i); + /* Make sure the text data is all put into one contiguous piece for decoding*/ + change.normalize(); + String plainString = ""; + int j = 0; + for(NodeList children = change.getChildNodes(); + children != null && j < children.getLength(); + j++){ + Node child = children.item(j); + if(child instanceof CDATASection || child instanceof Text){ + plainString += child.getNodeValue(); + } + } + + // Swap out this node for the decoded data + change.getParentNode().replaceChild(n.getOwnerDocument().createTextNode(plainString), change); + } + if(debug && node_list != null){ + debugPS.println("There were " + node_list.getLength() + + " XML Schema string encoded elements in the data"); + } + + // Parse the MOBY XML document payload + responseNode.normalize(); + NodeList children = responseNode.getChildNodes(); + if(children == null){ + throw new MobyException("The MOBY payload has no contents at all"); + } + if(children.getLength() != 1){ + debugPS.println("Warning: MOBY Payload appears to have more than " + + "just text in it, skipping the non-text sections"); + } + + responseString = ""; + for(int j = 0; j < children.getLength(); j++){ + Node child = children.item(j); + if(child instanceof CDATASection || child instanceof Text){ + responseString += child.getNodeValue(); } - return domDoc.getDocumentElement(); } - return null; //Shouldn't get here + + if(responseString.length() == 0){ + throw new MobyException("The MOBY payload has no text contents at all"); + } + + Document domDoc = null; + try{ + domDoc = docBuilder.parse(new StringBufferInputStream(responseString)); + } catch(org.xml.sax.SAXException saxe){ + throw new MobyException("The SOAP payload defining the MOBY Result " + + "could not be parsed: " + saxe); + } catch(java.io.IOException ioe){ + throw new MobyException("The SOAP payload defining the MOBY Result " + + " could not be read (from a String!)" + ioe); + } + + // release resources related to the Xpath execution, since we won't be using this doc anymore + releaseXPath(n); + + return domDoc.getDocumentElement(); } @@ -492,7 +598,7 @@ if(debug){ debugPS.println("Aha! Got " + response_list.getLength() + " mobyContent response elements"); } - // Do data deserialization for each response's mobyData + // Do data decoding for each response's mobyData for(int i = 0; i < response_list.getLength(); i++){ Node response = response_list.item(i); From gordonp at pub.open-bio.org Wed Jul 7 12:07:47 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed, 7 Jul 2004 12:07:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071607.i67G7ln4032248@pub.open-bio.org> gordonp Wed Jul 7 12:07:46 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv32223 Modified Files: ChangeLog Log Message: Recorded fixes to MOBYRequest moby-live/Java/docs ChangeLog,1.15,1.16 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/05/20 16:23:15 1.15 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/07/07 16:07:46 1.16 @@ -1,3 +1,9 @@ +2004-07-07 Paul Gordon + + * Modifications to MobyRequest to handle Axis 1.1beta, and a variety of + encoding schemes (base64 and XSD string) and namespaces (1999 and 2001 + XSD, MOBY transport) + 2004-05-20 Paul Gordon * Added full working example of service discovery and invocation in From mwilkinson at pub.open-bio.org Thu Jul 8 20:21:53 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 20:21:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690LrIk005683@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY/Adaptor/moby Modified Files: queryapi.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/06/24 22:32:39 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/07/09 00:21:53 1.2 @@ -16,12 +16,7 @@ dbname => [undef, 'read/write'], port => [undef, 'read/write'], proxy => [undef, 'read/write'], - sourcetype => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], - url => [undef, 'read/write'], - _implementation => [undef, 'read/write'], # this is the implementation of the API, e.g. mysql - - dbh => [undef, 'read/write'], # once all the calls are converttd remove this! It should not be accessible from outside!!! - + url => [undef, 'read/write'], ); #_____________________________________________________________ @@ -41,10 +36,56 @@ } # List of names of all specified object attributes - sub _standard_keys { + sub _standard_keys_a { keys %_attr_data; } + sub username { + my ($self, $arg) = @_; + $self->{username} = $arg if defined $arg; + return $self->{username}; + } + sub password { + my ($self, $arg) = @_; + $self->{password} = $arg if defined $arg; + return $self->{password}; + } + sub dbname { + my ($self, $arg) = @_; + $self->{dbname} = $arg if defined $arg; + return $self->{dbname}; + } + sub port { + my ($self, $arg) = @_; + $self->{port} = $arg if defined $arg; + return $self->{port}; + } + sub proxy { + my ($self, $arg) = @_; + $self->{proxy} = $arg if defined $arg; + return $self->{proxy}; + } + sub sourcetype { + my ($self, $arg) = @_; + $self->{sourcetype} = $arg if defined $arg; + return $self->{sourcetype}; + } + sub url { + my ($self, $arg) = @_; + $self->{url} = $arg if defined $arg; + return $self->{url}; + } + sub _implementation { + my ($self, $arg) = @_; + $self->{'_implementation'} = $arg if defined $arg; + return $self->{'_implementation'}; + } + sub dbh { + my ($self, $arg) = @_; + $self->{dbh} = $arg if defined $arg; + return $self->{dbh}; + } + } sub new { @@ -54,7 +95,7 @@ my $self = bless {}, $class; - foreach my $attrname ( $self->_standard_keys ) { + foreach my $attrname ( $self->_standard_keys_a ) { if (exists $args{$attrname} && defined $args{$attrname}) { $self->{$attrname} = $args{$attrname} } elsif ($caller_is_obj) { @@ -62,95 +103,88 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - - my $source = $self->sourcetype; - my $datasource = $source->new(adaptor => $self); - unless ($datasource) { - print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; - return undef; - } - $self->_implementation($datasource); - - # the lines below should be removed, since this should be pushed down into the implementation - ############################################################## - unless ($datasource->dbh) { - print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; - return undef; - } - - $self->dbh($datasource->dbh); - ############################################################# - return $self; } sub insert_collection_input { - my ($self, %args) = @_; - my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ - # this should be dropped down into the mysql.pm module?? probably... - $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); - my $id=$self->dbh->{mysql_insertid}; - return $id; - } + die "insert_collection_input not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + #if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # # this should be dropped down into the mysql.pm module?? probably... + # $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + # my $id=$self->dbh->{mysql_insertid}; + # return $id; + #} } sub insert_collection_output { - my ($self, %args) = @_; - my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ - # this should be dropped down into the mysql.pm module?? probably... - $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); - my $id=$self->dbh->{mysql_insertid}; - return $id; - } + die "insert_collection_output not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + #if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # # this should be dropped down into the mysql.pm module?? probably... + # $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + # my $id=$self->dbh->{mysql_insertid}; + # return $id; + #} } sub insert_simple_input { - my ($self, %args) = @_; - my $dbh = $self->dbh; - - $dbh->do("insert into simple_input - (object_type_uri, - namespace_type_uris, - article_name, - service_instance_id, - collection_input_id) - values (?,?,?,?,?)", - undef, - ($args{object_type_uri}, - $args{namespace_type_uris}, - $args{article_name}, - $args{service_instance_id}, - $args{collection_input_id})); - my $id=$dbh->{mysql_insertid}; - return $id; + die "insert_simple_input not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + # + #$dbh->do("insert into simple_input + # (object_type_uri, + # namespace_type_uris, + # article_name, + # service_instance_id, + # collection_input_id) + # values (?,?,?,?,?)", + # undef, + # ($args{object_type_uri}, + # $args{namespace_type_uris}, + # $args{article_name}, + # $args{service_instance_id}, + # $args{collection_input_id})); + #my $id=$dbh->{mysql_insertid}; + #return $id; } sub insert_simple_output { - my ($self, %args) = @_; - my $dbh = $self->dbh; - - $dbh->do("insert into simple_output - (object_type_uri, - namespace_type_uris, - article_name, - service_instance_id, - collection_output_id) - values (?,?,?,?,?)", - undef, - ($args{object_type_uri}, - $args{namespace_type_uris}, - $args{article_name}, - $args{service_instance_id}, - $args{collection_output_id})); - my $id=$dbh->{mysql_insertid}; - return $id; + die "insert_simple_output not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + # + #$dbh->do("insert into simple_output + # (object_type_uri, + # namespace_type_uris, + # article_name, + # service_instance_id, + # collection_output_id) + # values (?,?,?,?,?)", + # undef, + # ($args{object_type_uri}, + # $args{namespace_type_uris}, + # $args{article_name}, + # $args{service_instance_id}, + # $args{collection_output_id})); + #my $id=$dbh->{mysql_insertid}; + #return $id; } +sub query_service_instance { + die "query_service_instance not implemented in adaptor\n"; +} + +sub insert_service_instance { + die "insert_service_instance not implemented in adaptor\n"; +} + sub _dump { my ($self) = @_; @@ -160,37 +194,37 @@ } sub DESTROY {} - -sub AUTOLOAD { - no strict "refs"; - my ($self, $newval) = @_; - - $AUTOLOAD =~ /.*::(\w+)/; - - my $attr=$1; - if ($self->_accessible($attr,'write')) { - - *{$AUTOLOAD} = sub { - if (defined $_[1]) { $_[0]->{$attr} = $_[1] } - return $_[0]->{$attr}; - }; ### end of created subroutine - -### this is called first time only - if (defined $newval) { - $self->{$attr} = $newval - } - return $self->{$attr}; - - } elsif ($self->_accessible($attr,'read')) { - - *{$AUTOLOAD} = sub { - return $_[0]->{$attr} }; ### end of created subroutine - return $self->{$attr} } - - - # Must have been a mistake then... - croak "No such method: $AUTOLOAD"; -} - +# +#sub AUTOLOAD { +# no strict "refs"; +# my ($self, $newval) = @_; +# +# $AUTOLOAD =~ /.*::(\w+)/; +# +# my $attr=$1; +# if ($self->_accessible($attr,'write')) { +# +# *{$AUTOLOAD} = sub { +# if (defined $_[1]) { $_[0]->{$attr} = $_[1] } +# return $_[0]->{$attr}; +# }; ### end of created subroutine +# +#### this is called first time only +# if (defined $newval) { +# $self->{$attr} = $newval +# } +# return $self->{$attr}; +# +# } elsif ($self->_accessible($attr,'read')) { +# +# *{$AUTOLOAD} = sub { +# return $_[0]->{$attr} }; ### end of created subroutine +# return $self->{$attr} } +# +# +# # Must have been a mistake then... +# croak "No such method: $AUTOLOAD"; +#} +# 1; From mwilkinson at pub.open-bio.org Thu Jul 8 20:21:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 20:21:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690Lshx005702@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/06/24 22:32:39 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/09 00:21:53 1.2 @@ -1,8 +1,13 @@ package MOBY::Adaptor::moby::queryapi::mysql; use strict; -use vars qw($AUTOLOAD); +use vars qw($AUTOLOAD @ISA); use Carp; +use MOBY::Adaptor::moby::queryapi; +use DBI; +use DBD::mysql; + + at ISA = qw{MOBY::Adaptor::moby::queryapi}; # implements the interface { #Encapsulated class data @@ -12,7 +17,6 @@ my %_attr_data = # DEFAULT ACCESSIBILITY ( driver => ["DBI:mysql", 'read/write'], - adaptor => [undef, 'read/write'], # I think this causes a circular reference... dbh => [undef, 'read/write'], ); @@ -38,15 +42,26 @@ keys %_attr_data; } + sub driver { + my ($self, $arg) = @_; + $self->{driver} = $arg if defined $arg; + return $self->{driver}; + } + sub dbh { + my ($self, $arg) = @_; + $self->{dbh} = $arg if defined $arg; + return $self->{dbh}; + } + } sub new { my ($caller, %args) = @_; + my $self = $caller->SUPER::new(%args); + my $caller_is_obj = ref($caller); my $class = $caller_is_obj || $caller; - my $self = bless {}, $class; - foreach my $attrname ( $self->_standard_keys ) { if (exists $args{$attrname} && defined $args{$attrname}) { $self->{$attrname} = $args{$attrname} } @@ -55,58 +70,194 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - + return unless $self->driver; - my $driver = $self->driver; - my $username = $self->adaptor->username; - my $password = $self->adaptor->password; - my $port = $self->adaptor->port; - my $url = $self->adaptor->url; - my $dbname = $self->adaptor->dbname; + my $driver = $self->driver; # inherited from the adaptorI (queryapi) + my $username = $self->username; + my $password = $self->password; + my $port = $self->port; + my $url = $self->url; + my $dbname = $self->dbname; my ($dsn) = "$driver:$dbname:$url:$port"; - #my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database"; - +# print STDERR "\n\nconnectiung to $driver:$dbname:$url:$port\n\n"; my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database"; - return undef unless $dbh; - $self->dbh($dbh); + + + ############################################################## + unless ($dbh) { + print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; + return undef; + } + + $self->dbh($dbh); + ############################################################# + + return undef unless $self->dbh; return $self; } -sub DESTROY {} +sub insert_collection_input { + my ($self, %args) = @_; + my $dbh = $self->dbh; + if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # this should be dropped down into the mysql.pm module?? probably... + $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + my $id=$self->dbh->{mysql_insertid}; + return $id; + } +} -sub AUTOLOAD { - no strict "refs"; - my ($self, $newval) = @_; - - $AUTOLOAD =~ /.*::(\w+)/; - - my $attr=$1; - if ($self->_accessible($attr,'write')) { - - *{$AUTOLOAD} = sub { - if (defined $_[1]) { $_[0]->{$attr} = $_[1] } - return $_[0]->{$attr}; - }; ### end of created subroutine - -### this is called first time only - if (defined $newval) { - $self->{$attr} = $newval +sub insert_collection_output { + my ($self, %args) = @_; + my $dbh = $self->dbh; + if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # this should be dropped down into the mysql.pm module?? probably... + $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + my $id=$self->dbh->{mysql_insertid}; + return $id; } - return $self->{$attr}; +} - } elsif ($self->_accessible($attr,'read')) { +sub insert_simple_input { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do("insert into simple_input + (object_type_uri, + namespace_type_uris, + article_name, + service_instance_id, + collection_input_id) + values (?,?,?,?,?)", + undef, + ($args{object_type_uri}, + $args{namespace_type_uris}, + $args{article_name}, + $args{service_instance_id}, + $args{collection_input_id})); + my $id=$dbh->{mysql_insertid}; + return $id; +} - *{$AUTOLOAD} = sub { - return $_[0]->{$attr} }; ### end of created subroutine - return $self->{$attr} } +sub insert_simple_output { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do("insert into simple_output + (object_type_uri, + namespace_type_uris, + article_name, + service_instance_id, + collection_output_id) + values (?,?,?,?,?)", + undef, + ($args{object_type_uri}, + $args{namespace_type_uris}, + $args{article_name}, + $args{service_instance_id}, + $args{collection_output_id})); + my $id=$dbh->{mysql_insertid}; + return $id; - # Must have been a mistake then... - croak "No such method: $AUTOLOAD"; } +sub query_service_instance { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? + q{select + service_instance_id, + category, + serviceName, + service_type_uri, + authority.authority_uri, + url, + service_instance.contact_email, + authoritative, + description + from service_instance, authority + where + service_instance.authority_id = authority.authority_id + and servicename=? and authority.authority_uri = ? + }, + undef,($args{servicename}, $args{authURI})); + return undef unless $serviceid; + return {serviceid => $serviceid, + category => $category, + name => $name, + servcetype => $typeURI, + authURI => $authURI, + url => $url, + email => $email, + authoritative => $authoritative, + desc => $desc, + }; +} + + +sub insert_service_instance { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, + undef, + $args{'category'}, + $args{'servicename'}, + $args{'service_type_uri'}, + $args{'authority_id'}, + $args{'url'}, + $args{'contact_email'}, + $args{'authoritative'}, + $args{'description'}); + + my $id = $dbh->{mysql_insertid}; + return $id; +} + + + +sub _checkURI { + +# my $uri = "http://www.ics.uci.edu/pub/ietf/uri/#Related"; +#print "$1, $2, $3, $4, $5, $6, $7, $8, $9" if +# $uri =~ m{^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?}; +# +#The license for this recipe is available here. +# +#Discussion: +# +#If the match is successful, a URL such as +# +#http://www.ics.uci.edu/pub/ietf/uri/#Related +# +#will be broken down into the following group match variables: +# +#$1 = http: +#$2 = http +#$3 = //www.ics.uci.edu +#$4 = www.ics.uci.edu +#$5 = /pub/ietf/uri/ +#$6 = +#$7 = +#$8 = #Related +#$9 = Related +# +#In general, this regular expression breaks a URI down into the following parts, +#as defined in the RFC: +# +#scheme = $2 +#authority = $4 +#path = $5 +#query = $7 +#fragment = $9 + +} + +sub DESTROY {} 1; From mwilkinson at pub.open-bio.org Thu Jul 8 20:21:53 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 20:21:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690LrJD005664@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY Modified Files: Central.pm Config.pm dbConfig.pm service_instance.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY Central.pm,1.131,1.132 Config.pm,1.3,1.4 dbConfig.pm,1.2,1.3 service_instance.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.131 retrieving revision 1.132 diff -u -r1.131 -r1.132 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/06/24 22:32:38 1.131 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/09 00:21:53 1.132 @@ -1942,15 +1942,16 @@ sub retrieveService { my ($pkg, $payload) = @_; + # the payload here is actually the full XML from the findService call above... #return "NOT YET IMPLEMENTED"; - my ($AuthURI, $serviceName) = &_retrieveServicePayload($payload); + my ($AuthURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML) = &_retrieveServicePayload($payload); unless ($AuthURI && $serviceName){return ""} my $SI = MOBY::service_instance->new(authority_uri => $AuthURI, servicename => $serviceName); my $wsdls; return "" unless ($SI); if ($SI->category eq 'moby'){ - my $wsdl = &_getServiceWSDL($SI); + my $wsdl = &_getServiceWSDL($SI, $InputXML, $OutputXML, $SecondaryXML); if ($wsdl){ $wsdls .= "\n"; } @@ -1976,7 +1977,27 @@ $serviceName = $x->item($n)->getAttributeNode("serviceName"); # may or may not have a name if ($serviceName){$serviceName = $serviceName->getValue()} } - return ($authURI, $serviceName); + + my $INPUT = $doc->getElementsByTagName("Input"); + my $InputXML = ""; + if ($INPUT->item(0)){ + $InputXML = $INPUT->item(0)->toString; + } + + my $OUTPUT = $doc->getElementsByTagName("Output"); + my $OutputXML = ""; + if ($OUTPUT->item(0)){ + $OutputXML = $OUTPUT->item(0)->toString; + } + + my $SECONDARY = $doc->getElementsByTagName("Output"); + my $SecondaryXML = ""; + if ($SECONDARY->item(0)){ + $SecondaryXML = $SECONDARY->item(0)->toString; + } + + return ($authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML); + } @@ -2571,7 +2592,7 @@ sub _getServiceWSDL { - my ($SI) = @_; + my ($SI, $InputXML, $OutputXML, $SecondaryXML) = @_; # the lines below causes no end of grief. It is now in a variable. #open (WSDL, "./MOBY/Central_WSDL_SandR.wsdl") || die "can't open WSDL file for search and replace\n"; #my $wsdl = join "", (); @@ -2586,8 +2607,13 @@ my $URL = $SI->url; my $IN = "NOT_YET_DEFINED_INPUTS"; my $OUT = "NOT_YET_DEFINED_OUTPUTS"; - my $INxsd = ""; - my $OUTxsd=""; + + my $INxsd = &_getInputXSD($InputXML, $SecondaryXML); + my $OUTxsd = &_getOutputXSD($OutputXML); + + $INxsd ||= ""; + $OUTxsd ||=""; + $wsdl =~ s/MOBY__SERVICE__NAME__/$serviceName/g; # replace all of the goofy portbindingpottype crap $wsdl =~ s/\<\!\-\-\s*MOBY__SERVICE__DESCRIPTION\s*\-\-\>/Authority: $AuthURI - $desc/g; # add a sensible description $wsdl =~ s/MOBY__SERVICE__URL/$URL/g; # the URL to the service @@ -3045,6 +3071,125 @@ END +=head2 _getInputXSD + + name : _getInputXSD($InputXML, $SecondaryXML) + function: to get an XSD describing the input to a MOBY Service, + e.g. to use in a WSDL document + args : (see _serviceListResponse code above for full details of XML) + $InputXML - the ... block of a findService + response message + + $SecondaryXML - the ... + fragment of a findService response message + + returns : XSD fragment of XML (should not return an XML header!) + notes : the structure of an Input block is as follows: + + + + + the structure of a secondaryArticle block is as follows: + + + + + +=over + +=item * Simple + + + ObjectOntologyTerm + NamespaceTerm + ... + + +=item * Collection note that articleName of the contained Simple objects is not required, and is ignored. + + + + ...... + ...... + + +=item * Secondary + + + + INT|FLOAT|STRING + ... + ... + ... + ... + ... + + +=back + +=cut + + +sub _getInputXSD { + my ($Input, $Secondary) =@_; + my $XSD; + + + return $XSD; +} + +=head2 _getOuputXSD + + name : _getOutputXSD($OutputXML) + function: to get an XSD describing the output from a MOBY Service + e.g. to use in a WSDL document + args : (see _serviceListResponse code above for full details) + $InputXML - the ... block of a findService + response message + + $SecondaryXML - the ... + fragment of a findService response message + + returns : XSD fragment of XML (should not return an XML header!) + notes : the structure of an Output block is as follows: + + + + +=over + +=item * Simple + + + ObjectOntologyTerm + NamespaceTerm + ... + + +=item * Collection note that articleName of the contained Simple objects is not required, and is ignored. + + + + ...... + ...... + + +=back + +=cut + +sub _getOutputXSD { + my ($Output) =@_; + my $XSD; + + + return $XSD; +} + 1; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/06/24 22:32:38 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/07/09 00:21:53 1.4 @@ -74,7 +74,7 @@ } my $file = $ENV{MOBY_CENTRAL_CONFIG}; - $file || die "can't open MOBY Configuration file $!\n"; + (-e $file) || die "can't open MOBY Configuration file $!\n"; chomp $file; if ((-e $file) && (!(-d $file))){ @@ -106,27 +106,22 @@ if ($self->{"${source}Adaptor"}){return $self->{"${source}Adaptor"}}; # read from cache - my $username = $self->$source->{username}; # $self->source returns a MOBY::dbConfig object + my $username = $self->$source->{username}; # $self->$source returns a MOBY::dbConfig object my $password = $self->$source->{password}; my $port = $self->$source->{port}; my $dbname = $self->$source->{dbname}; my $url = $self->$source->{url}; my $adaptor = $self->$source->{adaptor}; - my $sourcetype = $self->$source->{sourcetype}; eval "require $adaptor"; return undef if $@; - eval "require $sourcetype"; - return undef if $@; - my $ADAPTOR = $adaptor->new( # by default, this is queryapi - source => $source, + my $ADAPTOR = $adaptor->new( # by default, this is queryapi::mysql username => $username, password => $password, port => $port, dbname => $dbname, url => $url, - sourcetype => $sourcetype, ); if ($ADAPTOR){ $self->{"${source}Adaptor"} = $ADAPTOR; # cache it =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm 2004/06/29 16:23:59 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm 2004/07/09 00:21:53 1.3 @@ -18,8 +18,7 @@ dbname => [undef, 'read/write'], port => [undef, 'read/write'], proxy => [undef, 'read/write'], - adaptor => ["MOBY::Adaptor::moby::queryapi", 'read/write'], - sourcetype => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], + adaptor => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], url => [undef, 'read/write'], section => [undef, 'read/write'], ); @@ -44,7 +43,7 @@ sub _standard_keys { keys %_attr_data; } - # List of names of all specified object attributes + sub database_title { my ($self, $val) = @_; $self->section_title($val) if $val; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/06/24 22:32:38 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/09 00:21:53 1.6 @@ -8,6 +8,7 @@ use MOBY::central_db_connection; use MOBY::OntologyServer; use MOBY::authority; +use MOBY::Config; #@ISA = qw(MOBY::central_db_connection); # can't do this yet... @@ -74,14 +75,6 @@ description => [undef, 'read/write'], registry => ['MOBY_Central', 'read/write'], test => [0, 'read/write'], # toggles create or test_existence behaviour - - username => ["mobycentral", 'read/write'], - password => ["mobycentral", 'read/write'], - dbname => ["mobycentral", 'read/write'], - host => ["localhost", 'read/write'], - port => [3306, 'read/write'], - dbh => [undef, 'read/write'], - ); #_____________________________________________________________ @@ -147,14 +140,23 @@ (defined $val) && ($self->{description} = $val); return $self->{description} } + + sub dbh { + $CONFIG ||=MOBY::Config->new; # exported by Config.pm + my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral')->dbh; + } + sub adaptor { + $CONFIG ||=MOBY::Config->new; # exported by Config.pm + my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral'); + } } -sub _dbh { - my ($self) = @_; - - my $central_connect = MOBY::central_db_connection->new(); - $self->dbh($central_connect->dbh); -} +#sub _dbh { +# my ($self) = @_; +# +# my $central_connect = MOBY::central_db_connection->new(); +# $self->dbh($central_connect->dbh); +#} sub new { my ($caller, %args) = @_; @@ -186,13 +188,15 @@ return undef unless $self->authority_uri; return undef unless $self->servicename; - $self->_dbh(); - return undef unless $self->dbh; - my $dbh = $self->dbh; + #$self->_dbh(); + #return undef unless $self->dbh; + #my $dbh = $self->dbh; if ($self->test){ return $self->service_instance_exists} - $self->authority($self->_get_authority()); + $self->authority($self->_get_authority()); # this might not be necessary - it simply converts auth_uri to auth_id and v.v.? + # it actually is necessary for the moment. We need to put the logic of determining + # service id into the mysql.pm module!! if ($self->service_type){ my $OE = MOBY::OntologyServer->new(ontology => 'service'); @@ -201,54 +205,43 @@ ($self->service_type =~ /urn:lsid/)?$self->service_type_uri($self->service_type):$self->service_type_uri($servicetypeURI); } - my ($serviceid, $category, $name, $typeURI, $authid,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? - q{select - service_instance_id, - category, - serviceName, - service_type_uri, - authority_id, - url, - contact_email, - authoritative, - description - from service_instance where servicename=? and authority_id=?}, - undef,($self->servicename, $self->authority->authority_id)); + my $existing_service = $self->adaptor->query_service_instance (servicename => $self->servicename, authURI => $self->authority_uri); + + - if ((defined $serviceid) # if it exists, you are not allowed to have passed anything other than service name and authorityURI + if (($existing_service) # if it exists, you are not allowed to have passed anything other than service name and authorityURI && ((defined $self->category) || (defined $self->service_type) || (defined $self->url) || (defined $self->contact_email) || (defined $self->description))){ return -1; # no no no, not alowed to do that! I will not give you an object - } elsif (defined $serviceid){ # if service exists, then instantiate it from the database retrieval we just did - $self->service_instance_id($serviceid); - $self->category($category); - $self->service_type($typeURI); - $self->url($url); - $self->contact_email($email); - $self->description($desc); - $self->authority($self->_get_authority); + } elsif ($existing_service){ # if service exists, then instantiate it from the database retrieval we just did + $self->service_instance_id($existing_service->{'serviceid'}); + $self->category($existing_service->{'category'}); + $self->service_type($existing_service->{'servicetype'}); + $self->url($existing_service->{'url'}); + $self->contact_email($existing_service->{'email'}); + $self->description($existing_service->{'desc'}); + $self->authority($existing_service->{'authURI'}); $self->{__exists__} = 1; # this service already existed - } elsif (!(defined $serviceid) # if it doesn't exist + } elsif (!($existing_service) # if it doesn't exist && (defined $self->category) # and you have given me things I need to create it && (defined $self->service_type) && (defined $self->url) && (defined $self->contact_email) && (defined $self->description)) { # then create it de novo if we have enough information - $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, - undef, - $self->category, - $self->servicename, - $self->service_type_uri, - $self->authority->authority_id, - $self->url, - $self->contact_email, - $self->authoritative, - $self->description); - $self->service_instance_id($dbh->{mysql_insertid}); + my $id = $self->adaptor->insert_service_instance( + category => $self->category, + servicename => $self->servicename, + service_type_uri => $self->service_type_uri, + authority_id => $self->authority_id, + url => $self->url, + contact_email => $self->contact_email, + authoritative => $self->authoritative, + description => $self->description); + $self->service_instance_id($id); $self->{__exists__} = 1; # this service now exists } else { # if it doesn't exist, and you havne't given me anyting I need to create it, then bail out return undef; @@ -263,6 +256,8 @@ unless ($self->{__exists__}){ return undef } + $CONFIG ||=MOBY::Config->new; + $dbh->do(q{delete from service_instance where service_instance_id = ?},undef,$self->service_instance_id); $dbh->do(q{delete from simple_input where service_instance_id = ?},undef,$self->service_instance_id); $dbh->do(q{delete from simple_output where service_instance_id = ?},undef,$self->service_instance_id); @@ -299,7 +294,7 @@ } -sub _get_authority { +sub _get_authority { # there's somethign fishy here... the authority.pm object already knows about authority_id and authorty_uri, doens't it? my ($self) = @_; my $dbh = $self->dbh; my $authority; From mwilkinson at pub.open-bio.org Thu Jul 8 20:21:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 20:21:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690Lsns005722@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv5633/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/06/16 19:07:34 1.17 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/09 00:21:53 1.18 @@ -213,19 +213,33 @@ ["Object", ['UglyNamespace']], # Simple ]), 24, 1); +my ($si, $reg) = $C->findService( + serviceName => "myfirstservice2" +); + +$si = $si->[0]; +my $wsdl = $C->retrieveService($si); +print $wsdl; +if ($wsdl && ($wsdl =~ /\deregisterService( serviceName => "myfirstservice2", authURI => "www.illuminae.com", - ), 25, 1); + ), 26, 1); TEST($C->deregisterService( serviceName => "myfirstservice2", authURI => "www.illuminae.com", - ), 26, 0); + ), 27, 0); TEST($C->deregisterService( serviceName => "myfirstservice", authURI => "www.illuminae.com", - ), 27, 1); + ), 28, 1); TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 28, 1); TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 29, 1); From mwilkinson at pub.open-bio.org Thu Jul 8 22:44:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 22:44:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090244.i692imAX006132@pub.open-bio.org> mwilkinson Thu Jul 8 22:44:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory pub.open-bio.org:/tmp/cvs-serv6113 Modified Files: LocalServices.pm Log Message: added the Union and Intersection services required by the Generation Challenge Program project. The existing client will not be able to discover nor use these services. moby-live/Perl/scripts/Services LocalServices.pm,1.63,1.64 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v retrieving revision 1.63 retrieving revision 1.64 diff -u -r1.63 -r1.64 --- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2004/06/29 16:24:00 1.63 +++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2004/07/09 02:44:48 1.64 @@ -1031,6 +1031,102 @@ } +sub ObjectUnion { + my ($caller, $data) = @_; # data is raw XML + my $MOBY_RESPONSE; + my $inputs= complexServiceInputParser($data); # thos converts it to XML::DOM objects + # hashref $input->{X} = [[COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]]...] + + return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (keys %{$inputs}); + + foreach my $queryID (keys %{$inputs}){ + my @inputlist = @{$inputs->{$queryID}}; + my $input1 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + my $input2 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + # input1 is now [COLLECTION(1), [DOM1, DOM2]] + my ($type1, $DOMS1) = @{$input1}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + my ($type2, $DOMS2) = @{$input2}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + + unless (($type1 == COLLECTION) && ($type2 == COLLECTION)){ # COLLECTION is a constant exported from MOBY::CommonSubs + $MOBY_RESPONSE .= collectionResponse([], "", $queryID) ; + next; + } + + my @DOMS1 = @{$DOMS1}; + my @DOMS2 = @{$DOMS2}; + my @ALLDOMS = (@DOMS1, @DOMS2); + + my %DOMHASH; + map {$DOMHASH{"$_"} = $_} @ALLDOMS; + + foreach my $dom1(@DOMS1){ + my $ns1 = getSimpleArticleNamespaceURI($dom1); + my ($id1) = getSimpleArticleIDs([$dom1]); + foreach my $dom2(@DOMS2){ + my $ns2 = getSimpleArticleNamespaceURI($dom2); + my ($id2) = getSimpleArticleIDs([$dom2]); + + if (($ns1 eq $ns2) && ($id1 eq $id2)){ + delete $DOMHASH{"$dom2"}; + } + } + } + my @simples; + while (my ($key, $DOM) = each %DOMHASH){ + push @simples, extractRawContent($DOM); + } + $MOBY_RESPONSE .= collectionResponse(\@simples, "UnionCollection", $queryID) ; + + } + #print $MOBY_RESPONSE; +# return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter)); +} + + +sub ObjectIntersection { + my ($caller, $data) = @_; # data is raw XML + my $MOBY_RESPONSE; + my $inputs= complexServiceInputParser($data); # thos converts it to XML::DOM objects + # hashref $input->{X} = [[COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]]...] + + return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (keys %{$inputs}); + + foreach my $queryID (keys %{$inputs}){ + my @inputlist = @{$inputs->{$queryID}}; + my $input1 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + my $input2 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + # input1 is now [COLLECTION(1), [DOM1, DOM2]] + my ($type1, $DOMS1) = @{$input1}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + my ($type2, $DOMS2) = @{$input2}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + + unless (($type1 == COLLECTION) && ($type2 == COLLECTION)){ # COLLECTION is a constant exported from MOBY::CommonSubs + $MOBY_RESPONSE .= collectionResponse([], "", $queryID) ; + next; + } + + my @DOMS1 = @{$DOMS1}; + my @DOMS2 = @{$DOMS2}; + my @gooddoms; + foreach my $dom1(@DOMS1){ + my $ns1 = getSimpleArticleNamespaceURI($dom1); + my ($id1) = getSimpleArticleIDs([$dom1]); + foreach my $dom2(@DOMS2){ + my $ns2 = getSimpleArticleNamespaceURI($dom2); + my ($id2) = getSimpleArticleIDs([$dom2]); + + if (($ns1 eq $ns2) && ($id1 eq $id2)){ + push @gooddoms, extractRawContent($dom1); + } + } + } + $MOBY_RESPONSE .= collectionResponse(\@gooddoms, "IntersectionCollection", $queryID) ; + + } + print $MOBY_RESPONSE; +# return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter)); +} + + ############################################################### ###################### for My Machine Only ################### sub _dbAccess { From mwilkinson at pub.open-bio.org Sun Jul 11 20:39:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun, 11 Jul 2004 20:39:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407120039.i6C0dbuC025484@pub.open-bio.org> mwilkinson Sun Jul 11 20:39:37 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv25446/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: tightening the business logic of MOBY Object registration, as I now see a few objects in the ontology that are invalid. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/09 00:21:53 1.18 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/12 00:39:37 1.19 @@ -1,13 +1,15 @@ #!/usr/bin/perl -w use MOBY::Client::Central; +my $v = 1 if ($ARGV[0] eq "verbose"); + sub TEST { # test of Registration object ($reg, $test, $expect) = @_; die "\a\a\aREG OBJECT MALFORMED" unless $reg; if ($reg->success == $expect){ - print "test $test\t\t[PASS]\n"; + print "test $test\t\t[PASS] ", ($v?($reg->message):""),"\n"; } else { - print "test $test\t\t[FAIL]\n",$reg->message,"\n\n"; + print "test $test\t\t[FAIL] ",$reg->message,"\n\n"; } } sub TEST2 { # test of ServiceInstance object listref @@ -31,8 +33,8 @@ ); -#reg first object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +#register with two ISA's -> should fail +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "blah.blah.blah", @@ -42,35 +44,56 @@ ['Object', 'articleName2']], HASA => [ ['Object', 'articleName3']]} + ), '1a', 0); + +#register with no ISA's -> should fail +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", + description => "a human-readable description of the object", + contactEmail => 'your at email.address', + authURI => "blah.blah.blah", + Relationships => { + HASA => [ + ['Object', 'articleName3']]} + ), '1b', 0); + +#reg first object class with a single ISA -> should pass +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", + description => "a human-readable description of the object", + contactEmail => 'your at email.address', + authURI => "blah.blah.blah", + Relationships => { + ISA => [ + ['Object', 'articleName2']], + HASA => [ + ['Object', 'articleName3']]} ), 1, 1); #reg duplicate object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['Object', 'article1'], - ['Object', 'articleName2']], + ['Object', 'article1'] + ], HASA => [ ['Object', 'articleName3']]} ), 2, 0); #reg second object class -TEST($C->registerObjectClass(objectType => "YetMoreCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject2", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['Object', 'article1'], ['Object', 'articleName2']], HASA => [ ['Object', 'articleName3']]} ), 3, 1); -TEST($C->registerServiceType(serviceType => "CrappyService", +TEST($C->registerServiceType(serviceType => "HypotheticalService1", description => "a human-readable description of the service", contactEmail => 'your at email.address', authURI => "blah.blah.blah", @@ -78,7 +101,7 @@ ISA => ['Retrieval','Analysis']} ), 4, 1); -TEST($C->registerServiceType(serviceType => "CrappyService", +TEST($C->registerServiceType(serviceType => "HypotheticalService1", description => "a human-readable description of the service", contactEmail => 'your at email.address', authURI => "blah.blah.blah", @@ -86,28 +109,28 @@ ISA => ['Retrieval','Analysis']} ), 5, 0); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 6, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 7, 0); -TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 8, 1); -TEST($C->deregisterServiceType(serviceType => "CrappyService"), 9, 1); -TEST($C->deregisterServiceType(serviceType => "CrappyService"), 10, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 6, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 7, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 8, 1); +TEST($C->deregisterServiceType(serviceType => "HypotheticalService1"), 9, 1); +TEST($C->deregisterServiceType(serviceType => "HypotheticalService1"), 10, 0); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your at address.here'), 11, 1); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your at address.here'), 12, 0); -TEST($C->deregisterNamespace(namespaceType =>'UglyNamespace'), 13, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 13, 1); #reg first object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", - contactEmail => 'your at email.address', + contactEmail => 'your at email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ @@ -115,19 +138,19 @@ ), 14, 1); #reg duplicate object class -TEST($C->registerObjectClass(objectType => "YetMoreCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject2", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['TotalCrap', 'article1']]} + ['HypotheticalObject1', 'article1']]} ), 15, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 16, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 16, 0); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your at address.here'), 17, 1); @@ -141,10 +164,10 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ - ['articleName1', [Object => ['UglyNamespace']]], # Simple + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], secondary => { parametername1 => { @@ -163,10 +186,10 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ - ['articleName1', [Object => ['UglyNamespace']]], # Simple + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], ), 19, 0); @@ -179,11 +202,11 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ -# ['articleName1', [[Object => ['UglyNamespace']]]], # Collection - ['articleName1', [Object => ['UglyNamespace']]], # Simple +# ['articleName1', [[Object => ['HypotheticalNamespace1']]]], # Collection + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], ), 20, 1); @@ -210,7 +233,7 @@ TEST2($C->findService( input =>[ - ["Object", ['UglyNamespace']], # Simple + ["Object", ['HypotheticalNamespace1']], # Simple ]), 24, 1); my ($si, $reg) = $C->findService( @@ -241,9 +264,9 @@ authURI => "www.illuminae.com", ), 28, 1); -TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 28, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 29, 1); -TEST($C->deregisterNamespace(namespaceType =>'UglyNamespace'), 30, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 28, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 29, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 30, 1); exit 0; From mwilkinson at pub.open-bio.org Sun Jul 11 20:39:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun, 11 Jul 2004 20:39:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407120039.i6C0dbk6025465@pub.open-bio.org> mwilkinson Sun Jul 11 20:39:37 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv25446/MOBY Modified Files: Central.pm Log Message: tightening the business logic of MOBY Object registration, as I now see a few objects in the ontology that are invalid. moby-live/Perl/MOBY Central.pm,1.132,1.133 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.132 retrieving revision 1.133 diff -u -r1.132 -r1.133 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/09 00:21:53 1.132 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/12 00:39:37 1.133 @@ -260,16 +260,20 @@ return &_error("Object name may not be an URN or URI","") if $1; } + my $ISAs; # validate that the final ontology will be valid by testing against existing relationships and such while (my ($reltype, $obj) = each %{$relationships}){ my ($success, $message, $URI) = $RelOntologyServer->relationshipExists(term => $reltype, ontology => 'object'); # success = 1 if it does - $success==0 && return &_error($message, $URI ); + $success==0 && return &_error($message, $URI ); foreach (@{$obj}){ + ++$ISAs if ($URI =~ /isa$/i); my ($objectType, $articleName) = @{$_}; my ($success, $message, $URI) = $OntologyServer->objectExists(term => $objectType); # success = 1 if it does $success==0 && return &_error($message, $URI ); } } + return &_error("Object must have exactly one ISA parent in the MOBY Object ontology") unless $ISAs == 1; + $clobber = defined($clobber)?$clobber:0; $clobber = 0 unless ($clobber eq 0 || $clobber eq 1 || $clobber eq 2); # safety! my ($exists, $exists_message, $URI) = $OntologyServer->objectExists(term => $term); # success = 1 if it does From gss at pub.open-bio.org Thu Jul 15 16:18:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152018.i6FKI1rq011930@pub.open-bio.org> gss Thu Jul 15 16:18:01 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv11909/S-MOBY/ref-impl/core/src/org/smoby/tools Added Files: ModelRetriever.java Log Message: New class moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools ModelRetriever.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:20:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:20:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152020.i6FKKb1I012013@pub.open-bio.org> gss Thu Jul 15 16:20:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients In directory pub.open-bio.org:/tmp/cvs-serv11988/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients Modified Files: SimpleProviderEngagerPanel.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/05/27 19:37:10 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/15 20:20:37 1.2 @@ -113,11 +113,19 @@ { Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML); MOBYProvider provider = parser.parseProvider(); - String graphURI = provider.getURI(); - HTTPRequest request = HTTPRequest.newPostRequest(graphURI); - request.addParameter("graph", graphString); - HTTPResponse response = request.send(); - outputArea.setText(response.getBody()); + + if (provider == null) + { + outputArea.setText("Couldn't parse provider"); + } + else + { + String graphURI = provider.getURI(); + HTTPRequest request = HTTPRequest.newPostRequest(graphURI); + request.addParameter("graph", graphString); + HTTPResponse response = request.send(); + outputArea.setText(response.getBody()); + } } catch (UnparsableGraphException e) { From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQk3E012103@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/.settings Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkwN012085@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkOl012067@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkuH012123@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQliU012249@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlDU012205@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlHB012225@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlUT012267@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlYq012162@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlxu012184@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQk15012141@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlH1012291@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmbX012374@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlZA012314@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmBr012332@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmaL012395@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmnC012457@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQm4Q012413@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQo1w012727@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnrV012522@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmSf012480@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnJe012541@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQn4m012564@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpN3012897@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnHE012607@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoG9012649@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQm9p012354@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpEM012918@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQncw012627@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnXG012498@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQos9012668@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpSD012772@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQqtU012963@pub.open-bio.org> gss Thu Jul 15 16:26:52 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQolE012709@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmF9012436@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpAW012857@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoZp012686@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQp4d012834@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpCE012790@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnON012586@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoqc012745@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpKD012879@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQp8C012808@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQq1p012983@pub.open-bio.org> gss Thu Jul 15 16:26:52 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQqpi012939@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFCk013305@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Added Files: index.html hello-world.n3 n3.html hello-world.rdf engage.html top-frame.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello index.html,NONE,1.1 hello-world.n3,NONE,1.1 n3.html,NONE,1.1 hello-world.rdf,NONE,1.1 engage.html,NONE,1.1 top-frame.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHYE013477@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use Added Files: HTTPException.html HTTPResponse.html HTTPRequest.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use HTTPException.html,NONE,1.1 HTTPResponse.html,NONE,1.1 HTTPRequest.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGme013365@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util Added Files: RDFXMLSerialization.n3 Serialization.n3 N3Serialization.n3 index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util RDFXMLSerialization.n3,NONE,1.1 Serialization.n3,NONE,1.1 N3Serialization.n3,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREU4013154@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer Added Files: index.html search.html suggest.html dev-tools.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer index.html,NONE,1.1 search.html,NONE,1.1 suggest.html,NONE,1.1 dev-tools.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRE5o013190@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary Added Files: VocabularyDescription.html package-use.html MOBY.html package-frame.html package-tree.html package-summary.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary VocabularyDescription.html,NONE,1.1 package-use.html,NONE,1.1 MOBY.html,NONE,1.1 package-frame.html,NONE,1.1 package-tree.html,NONE,1.1 package-summary.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFmO013260@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files Added Files: index-7.html index-5.html index-12.html index-16.html index-11.html index-3.html index-1.html index-10.html index-14.html index-4.html index-9.html index-15.html index-8.html index-2.html index-6.html index-13.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files index-7.html,NONE,1.1 index-5.html,NONE,1.1 index-12.html,NONE,1.1 index-16.html,NONE,1.1 index-11.html,NONE,1.1 index-3.html,NONE,1.1 index-1.html,NONE,1.1 index-10.html,NONE,1.1 index-14.html,NONE,1.1 index-4.html,NONE,1.1 index-9.html,NONE,1.1 index-15.html,NONE,1.1 index-8.html,NONE,1.1 index-2.html,NONE,1.1 index-6.html,NONE,1.1 index-13.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREOr013137@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core Added Files: __Collection.n3 Subject.n3 Provider name oneLineDescription.n3 Subject hasMapping.n3 operatesOn Provider.n3 providerAboutURI.n3 __Collection subjectProperty.n3 __NonCollection objectProperty name.n3 subjectProperty Object.n3 keyword.n3 objectProperty.n3 __Bag operatesOn.n3 Graph __NonCollection.n3 keyword __Seq __Alt.n3 __Alt Graph.n3 oneLineDescription mapsTo.n3 __List.n3 mapsTo __Seq.n3 index.html __List providerAboutURI hasMapping __Bag.n3 Object Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core __Collection.n3,NONE,1.1 Subject.n3,NONE,1.1 Provider,NONE,1.1 name,NONE,1.1 oneLineDescription.n3,NONE,1.1 Subject,NONE,1.1 hasMapping.n3,NONE,1.1 operatesOn,NONE,1.1 Provider.n3,NONE,1.1 providerAboutURI.n3,NONE,1.1 __Collection,NONE,1.1 subjectProperty.n3,NONE,1.1 __NonCollection,NONE,1.1 objectProperty,NONE,1.1 name.n3,NONE,1.1 subjectProperty,NONE,1.1 Object.n3,NONE,1.1 keyword.n3,NONE,1.1 objectProperty.n3,NONE,1.1 __Bag,NONE,1.1 operatesOn.n3,NONE,1.1 Graph,NONE,1.1 __NonCollection.n3,NONE,1.1 keyword,NONE,1.1 __Seq,NONE,1.1 __Alt.n3,NONE,1.1 __Alt,NONE,1.1 Graph.n3,NONE,1.1 oneLineDescription,NONE,1.1 mapsTo.n3,NONE,1.1 __List.n3,NONE,1.1 mapsTo,NONE,1.1 __Seq.n3,NONE,1.1 index.html,NONE,1.1 __List,NONE,1.1 providerAboutURI,NONE,1.1 hasMapping,NONE,1.1 __Bag.n3,NONE,1.1 Object,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDBM013048@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api Added Files: deprecated-list.html overview-frame.html developer.html constant-values.html allclasses-noframe.html packages.html stylesheet.css allclasses-frame.html package-list help-doc.html serialized-form.html overview-summary.html overview-tree.html index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api deprecated-list.html,NONE,1.1 overview-frame.html,NONE,1.1 developer.html,NONE,1.1 constant-values.html,NONE,1.1 allclasses-noframe.html,NONE,1.1 packages.html,NONE,1.1 stylesheet.css,NONE,1.1 allclasses-frame.html,NONE,1.1 package-list,NONE,1.1 help-doc.html,NONE,1.1 serialized-form.html,NONE,1.1 overview-summary.html,NONE,1.1 overview-tree.html,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRD2P013064@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use Added Files: MOBYDocumentImpl.html MOBYProviderSetImpl.html MOBYDescriptorImpl.html MOBYObjectFactory.html MOBYNonNegativeIntegerConstraintImpl.html MOBYMappingElementImpl.html MOBYProviderImpl.html MOBYDateConstraintImpl.html MOBYNonPositiveIntegerConstraintImpl.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use MOBYDocumentImpl.html,NONE,1.1 MOBYProviderSetImpl.html,NONE,1.1 MOBYDescriptorImpl.html,NONE,1.1 MOBYObjectFactory.html,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.html,NONE,1.1 MOBYMappingElementImpl.html,NONE,1.1 MOBYProviderImpl.html,NONE,1.1 MOBYDateConstraintImpl.html,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREJE013172@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Added Files: .cvsignore web.xml Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDcJ013101@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use Added Files: MOBYGraph.html MOBYOntology.html MOBYSingleElement.html MOBYObject.html MOBYProviderSet.html MOBYSubject.html MOBYGraphNode.html MOBYMappingElement.html MOBYUnorderedCollection.html MOBYResource.html MOBYEnumeration.html MOBYCollection.html MOBYPropertyValueConstraint.html MOBYDocument.html MOBYLiteral.html MOBYDescriptor.html MOBYPropertyValueException.html MOBYProvider.html MOBYFixedCollection.html MOBYPropertyValue.html MOBYOrderedCollection.html MOBYResizableCollection.html MOBYPropertyValueStatement.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use MOBYGraph.html,NONE,1.1 MOBYOntology.html,NONE,1.1 MOBYSingleElement.html,NONE,1.1 MOBYObject.html,NONE,1.1 MOBYProviderSet.html,NONE,1.1 MOBYSubject.html,NONE,1.1 MOBYGraphNode.html,NONE,1.1 MOBYMappingElement.html,NONE,1.1 MOBYUnorderedCollection.html,NONE,1.1 MOBYResource.html,NONE,1.1 MOBYEnumeration.html,NONE,1.1 MOBYCollection.html,NONE,1.1 MOBYPropertyValueConstraint.html,NONE,1.1 MOBYDocument.html,NONE,1.1 MOBYLiteral.html,NONE,1.1 MOBYDescriptor.html,NONE,1.1 MOBYPropertyValueException.html,NONE,1.1 MOBYProvider.html,NONE,1.1 MOBYFixedCollection.html,NONE,1.1 MOBYPropertyValue.html,NONE,1.1 MOBYOrderedCollection.html,NONE,1.1 MOBYResizableCollection.html,NONE,1.1 MOBYPropertyValueStatement.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREjs013118@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Added Files: DiscoveryQuery.java URIInvestigator.java MissingPropertyException.java ProviderRemover.java MOBYProperties.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools DiscoveryQuery.java,NONE,1.1 URIInvestigator.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 ProviderRemover.java,NONE,1.1 MOBYProperties.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDJg013033@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph Added Files: MOBYSingleElement.html MOBYSubject.html MOBYResizableCollection.html MOBYPropertyValueException.html MOBYMappingElement.html MOBYOntology.html package-use.html MOBYPropertyValueStatement.html MOBYProviderSet.html MOBYEnumeration.html MOBYGraph.html MOBYObject.html MOBYFixedCollection.html package-tree.html MOBYOrderedCollection.html MOBYResource.html MOBYDocument.html MOBYLiteral.html MOBYUnorderedCollection.html package-summary.html package-frame.html MOBYPropertyValueConstraint.html MOBYProvider.html MOBYPropertyValue.html MOBYGraphNode.html MOBYCollection.html MOBYDescriptor.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph MOBYSingleElement.html,NONE,1.1 MOBYSubject.html,NONE,1.1 MOBYResizableCollection.html,NONE,1.1 MOBYPropertyValueException.html,NONE,1.1 MOBYMappingElement.html,NONE,1.1 MOBYOntology.html,NONE,1.1 package-use.html,NONE,1.1 MOBYPropertyValueStatement.html,NONE,1.1 MOBYProviderSet.html,NONE,1.1 MOBYEnumeration.html,NONE,1.1 MOBYGraph.html,NONE,1.1 MOBYObject.html,NONE,1.1 MOBYFixedCollection.html,NONE,1.1 package-tree.html,NONE,1.1 MOBYOrderedCollection.html,NONE,1.1 MOBYResource.html,NONE,1.1 MOBYDocument.html,NONE,1.1 MOBYLiteral.html,NONE,1.1 MOBYUnorderedCollection.html,NONE,1.1 package-summary.html,NONE,1.1 package-frame.html,NONE,1.1 MOBYPropertyValueConstraint.html,NONE,1.1 MOBYProvider.html,NONE,1.1 MOBYPropertyValue.html,NONE,1.1 MOBYGraphNode.html,NONE,1.1 MOBYCollection.html,NONE,1.1 MOBYDescriptor.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRH9l013432@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Added Files: Test.html ParserTest.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Test.html,NONE,1.1 ParserTest.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDUa013082@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl Added Files: MOBYObjectFactory.html package-use.html package-summary.html MOBYNonNegativeIntegerConstraintImpl.html MOBYDescriptorImpl.html package-frame.html MOBYNonPositiveIntegerConstraintImpl.html package-tree.html MOBYProviderImpl.html MOBYProviderSetImpl.html MOBYDocumentImpl.html MOBYMappingElementImpl.html MOBYDateConstraintImpl.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl MOBYObjectFactory.html,NONE,1.1 package-use.html,NONE,1.1 package-summary.html,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.html,NONE,1.1 MOBYDescriptorImpl.html,NONE,1.1 package-frame.html,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.html,NONE,1.1 package-tree.html,NONE,1.1 MOBYProviderImpl.html,NONE,1.1 MOBYProviderSetImpl.html,NONE,1.1 MOBYDocumentImpl.html,NONE,1.1 MOBYMappingElementImpl.html,NONE,1.1 MOBYDateConstraintImpl.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGuP013335@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test Added Files: package-frame.html Test.html package-summary.html ParserTest.html package-tree.html package-use.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test package-frame.html,NONE,1.1 Test.html,NONE,1.1 package-summary.html,NONE,1.1 ParserTest.html,NONE,1.1 package-tree.html,NONE,1.1 package-use.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREeN013226@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http Added Files: package-summary.html HTTPResponse.html package-frame.html HTTPRequest.html package-tree.html package-use.html HTTPException.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http package-summary.html,NONE,1.1 HTTPResponse.html,NONE,1.1 package-frame.html,NONE,1.1 HTTPRequest.html,NONE,1.1 package-tree.html,NONE,1.1 package-use.html,NONE,1.1 HTTPException.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFLS013290@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org Added Files: .project .classpath .mymetadata Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org .project,NONE,1.1 .classpath,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREpq013206@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot Added Files: index.html tech-overview.html log4j.properties help1.jpg help.html about.html smoby.example.properties Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot index.html,NONE,1.1 tech-overview.html,NONE,1.1 log4j.properties,NONE,1.1 help1.jpg,NONE,1.1 help.html,NONE,1.1 about.html,NONE,1.1 smoby.example.properties,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIL4013662@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Added Files: greeting greeting.n3 Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies greeting,NONE,1.1 greeting.n3,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGq5013320@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev Added Files: MOBYGraphValidationServlet.java ProviderListServlet.java OWLValidationServlet.java GraphConversionServlet.java RepositoryPrintServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev MOBYGraphValidationServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 OWLValidationServlet.java,NONE,1.1 GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGE8013380@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Added Files: HelloWorldServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGAs013410@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies Added Files: index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHe2013507@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Added Files: Util.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Util.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRG0r013350@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet Added Files: package-frame.html AbstractMobyServlet.html ParameterException.html package-summary.html package-use.html ParamReader.html package-tree.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet package-frame.html,NONE,1.1 AbstractMobyServlet.html,NONE,1.1 ParameterException.html,NONE,1.1 package-summary.html,NONE,1.1 package-use.html,NONE,1.1 ParamReader.html,NONE,1.1 package-tree.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHPx013583@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Added Files: DiscoveryServlet.java KeywordSearchServlet.java BaseServlet.java ProviderInvestigationServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets DiscoveryServlet.java,NONE,1.1 KeywordSearchServlet.java,NONE,1.1 BaseServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIvF013645@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save Added Files: index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIBQ013599@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources Added Files: inherit.gif Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources inherit.gif,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFrh013275@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter Added Files: index.html top-frame.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter index.html,NONE,1.1 top-frame.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHva013453@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser Added Files: package-use.html package-frame.html UnparsableGraphException.html Parser.html package-summary.html NonCanonicalException.html package-tree.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser package-use.html,NONE,1.1 package-frame.html,NONE,1.1 UnparsableGraphException.html,NONE,1.1 Parser.html,NONE,1.1 package-summary.html,NONE,1.1 NonCanonicalException.html,NONE,1.1 package-tree.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHEI013492@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use Added Files: MOBY.html VocabularyDescription.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use MOBY.html,NONE,1.1 VocabularyDescription.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGsb013395@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use Added Files: ParameterException.html AbstractMobyServlet.html ParamReader.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use ParameterException.html,NONE,1.1 AbstractMobyServlet.html,NONE,1.1 ParamReader.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHCQ013531@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use Added Files: NonCanonicalException.html UnparsableGraphException.html Parser.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use NonCanonicalException.html,NONE,1.1 UnparsableGraphException.html,NONE,1.1 Parser.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRH73013550@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools Added Files: client.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools client.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHV7013568@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Added Files: StorageException.java StorageManager.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageException.java,NONE,1.1 StorageManager.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIKS013624@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/.settings Added Files: org.eclipse.core.resources.prefs Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings org.eclipse.core.resources.prefs,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREX1013243@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools Added Files: package-summary.html Util.html package-tree.html package-frame.html package-use.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools package-summary.html,NONE,1.1 Util.html,NONE,1.1 package-tree.html,NONE,1.1 package-frame.html,NONE,1.1 package-use.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:28:53 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:28:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152028.i6FKSrug013743@pub.open-bio.org> gss Thu Jul 15 16:28:53 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv13718/S-MOBY/ref-impl/core/src/org/smoby/parser Modified Files: Parser.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/06/18 21:38:27 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/15 20:28:53 1.5 @@ -6,6 +6,7 @@ import org.smoby.graph.*; import org.smoby.graph.impl.*; import org.smoby.parser.*; +import org.smoby.tools.ModelRetriever; import org.smoby.tools.Util; import org.smoby.vocabulary.*; import com.hp.hpl.jena.rdf.model.*; @@ -28,17 +29,12 @@ public final static String LANGUAGE_N3 = "N3"; /** - * Inference models containing inferred statements derived using - * rdfs:subClassOf relationships. + * Since models are stored in a single Jena model, we + * segregate the single model into multiple sub-models, + * each containing an rdf:type moby:Provider statement, + * plus all statements that are reachable from it. */ - private Map inferenceModels = new HashMap(); - - /** - * Return the inference model associated with a given plain model - */ - private InfModel getInferenceModel(Model model) { - return (InfModel) inferenceModels.get(model); - } + private List subModels = new ArrayList(); /** * Create and return a parser for parsing an N3 file @@ -136,8 +132,7 @@ subModel.setNsPrefixes(model.getNsPrefixMap()); Resource subject = stmt.getSubject(); Util.addReachableStmts(model, subModel, subject, subject.getURI()); - inferenceModels.put(subModel, - ModelFactory.createRDFSModel(subModel)); + subModels.add(subModel); } } @@ -168,7 +163,7 @@ // Parse each provider // - Iterator it = inferenceModels.keySet().iterator(); + Iterator it = subModels.iterator(); while (it.hasNext()) { Model model = (Model) it.next(); @@ -374,13 +369,17 @@ /** * Return a list of statements for whom the subject is a given resource, - * whose predicates is a subproperty of moby:Property, and whose object + * whose predicate is a subproperty of moby:Property, and whose object * is a blank node. */ private List mobyPropertyStatementsOf(Resource res) { + // The statements to return + // List stmts = new ArrayList(); + // Iterate over the statements whose subjects are the resource + // StmtIterator it = res.listProperties(); while (it.hasNext()) { @@ -388,17 +387,16 @@ Property p = stmt.getPredicate(); RDFNode pval = stmt.getObject(); - Model model = res.getModel(); - Model inferenceModel = getInferenceModel(model); + // Try to retrieve a description of the property at + // its URI. + // + InfModel model = getPropertyModel(p); - if (model.contains(res, p, pval) && - inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property)) + if (isMobyProperty(p, model)) { MOBYPropertyValueStatement pvalStmt = MOBYObjectFactory.newPropertyValueStatement(stmt, model); - // See if the property - // Statement s = p.getProperty(RDFS.range); if ((s != null) && (s.getObject().canAs(Resource.class))) @@ -423,6 +421,33 @@ return stmts; } + /** + * Get the model describing a given property by doing a GET + * on its URI, and creating an inference model from it. + */ + private InfModel getPropertyModel(Property p) + { + Model model = ModelRetriever.retrieveModel(p.getURI()); + + if (model == null) { + return null; + } else { + return ModelFactory.createRDFSModel(model); + } + } + + /** + * Return whether or not the given property is a MOBY property. + * This will be true if there is a statement in the model saying + * that the property is an rdfs:subPropertyOf moby:Property. + */ + private boolean isMobyProperty(Property p, InfModel model) + { + return + model != null && + model.contains(p, RDFS.subPropertyOf, MOBY.Property); + } + private String getDataPropertyValue(Resource subject, Property property) { Statement s = subject.getModel().getProperty(subject, property); From gss at pub.open-bio.org Thu Jul 15 16:30:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUG2E013793@pub.open-bio.org> gss Thu Jul 15 16:30:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings In directory pub.open-bio.org:/tmp/cvs-serv13769/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 16:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIeY013882@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Added Files: citation-search.n3 citation-search.rdf Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citation-search.n3,NONE,1.1 citation-search.rdf,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIrT013846@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/05/27 15:31:31 1.10 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/15 20:30:18 1.11 @@ -19,7 +19,7 @@ /** * The provider description graph is stored in a file named "citationSearch" */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; + private final static String DESCRIPTION_GRAPH_FILE = "citation-search.rdf"; /** * Read the description graph from a file named "terms" in the From gss at pub.open-bio.org Thu Jul 15 16:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIjd013866@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF Modified Files: web.xml Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF web.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml 2004/06/10 23:13:44 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml 2004/07/15 20:30:18 1.3 @@ -13,7 +13,7 @@ CitationSearchServlet - /citationSearch + /citation-search From gss at pub.open-bio.org Thu Jul 15 16:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIU5013827@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings Added Files: org.eclipse.core.resources.prefs Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings org.eclipse.core.resources.prefs,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:31:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:31:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152031.i6FKV7bk013923@pub.open-bio.org> gss Thu Jul 15 16:31:07 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage In directory pub.open-bio.org:/tmp/cvs-serv13902/S-MOBY/ref-impl/queries/engage Added Files: engage-acmepubs-citation-search.rdf engage-acmepubs-citation-search.n3 Log Message: New queries moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citation-search.rdf,NONE,1.1 engage-acmepubs-citation-search.n3,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 16:28:04 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:28:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152028.i6FKS4n5013713@pub.open-bio.org> gss Thu Jul 15 16:28:04 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv13688/S-MOBY/ref-impl/core/src/org/smoby/vocabulary Modified Files: MOBY.java Log Message: Changed s-moby.org:8080 to semanticmoby.org moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/06/18 21:39:42 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/15 20:28:04 1.5 @@ -10,7 +10,7 @@ public static String getURI() { - return "http://www.s-moby.org:8080/terms/"; + return "http://www.semanticmoby.org/ontologies/core/"; } public static String getNsPrefix() From gss at pub.open-bio.org Thu Jul 15 16:54:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:54:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152054.i6FKsbhr014079@pub.open-bio.org> gss Thu Jul 15 16:54:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14054/S-MOBY/ref-impl/server/WebRoot Modified Files: domains.html Log Message: Minor fixes moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/06/17 17:35:52 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 20:54:37 1.5 @@ -55,7 +55,7 @@ www.acmepubs.com/citationSearch + "http://www.acmepubs.com:8080/citation-search">www.acmepubs.com/citation-search Provider description graph for acmepubs.com. Note that doing an HTTP GET on this URI @@ -83,11 +83,11 @@ www.megapubs.com/citationSearch + "http://www.megapubs.com:8080/citation-search">www.megapubs.com/citation-search Provider description graph for megapubs.com. The notes regarding the - www.acmepubs.com/citationSearch also apply to this URI.
+ www.acmepubs.com/citation-search also apply to this URI.
From gss at pub.open-bio.org Thu Jul 15 16:58:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:58:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152058.i6FKwINQ014126@pub.open-bio.org> gss Thu Jul 15 16:58:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14089/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 citation-search.n3 citation-search.rdf Log Message: Changed to be ASCII moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.7,1.8 citationSearch.n3,1.6,1.7 citation-search.n3,1.1,1.2 citation-search.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/06/16 18:50:59 1.7 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/07/15 20:58:18 1.8 @@ -1,37 +1,37 @@ - - - - - - - - - - - - - - - - - - AcmePubs Citation Search - Industry standard search - - - - - - - - - \ No newline at end of file + + + + + + + + + + + + + + + + + + AcmePubs Citation Search + Industry standard search + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/06/16 18:50:59 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/07/15 20:58:18 1.7 @@ -1,28 +1,28 @@ - at prefix acmepubs: . - at prefix acmeterms: . - at prefix pubs: . - at prefix go: . - at prefix sgd: . - at prefix moby: . - at prefix rdfs: . - at prefix rdf: . - at prefix owl: . - -acmepubs:citationSearch - a moby:Provider, pubs:citationSearch ; - moby:name "AcmePubs Citation Search" ; - moby:oneLineDescription "Industry standard search" ; - moby:operatesOn [ - a rdf:Bag ; - rdf:_1 [ - a moby:Graph ; - moby:hasMapping [ - a moby:Subject, go:GeneSymbol ; - acmeterms:geneSymbol _:bnode1 ; - moby:mapsTo [ - a moby:Object, sgd:LiteratureGuide ; - acmeterms:literatureGuideURI _:bnode2 - ] - ] - ] - ] . \ No newline at end of file + at prefix acmepubs: . + at prefix acmeterms: . + at prefix pubs: . + at prefix go: . + at prefix sgd: . + at prefix moby: . + at prefix rdfs: . + at prefix rdf: . + at prefix owl: . + +acmepubs:citationSearch + a moby:Provider, pubs:citationSearch ; + moby:name "AcmePubs Citation Search" ; + moby:oneLineDescription "Industry standard search" ; + moby:operatesOn [ + a rdf:Bag ; + rdf:_1 [ + a moby:Graph ; + moby:hasMapping [ + a moby:Subject, go:GeneSymbol ; + acmeterms:geneSymbol _:bnode1 ; + moby:mapsTo [ + a moby:Object, sgd:LiteratureGuide ; + acmeterms:literatureGuideURI _:bnode2 + ] + ] + ] + ] . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3 2004/07/15 20:30:18 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3 2004/07/15 20:58:18 1.2 @@ -1,28 +1,28 @@ - at prefix acmepubs: . - at prefix acmeterms: . - at prefix pubs: . - at prefix go: . - at prefix sgd: . - at prefix moby: . - at prefix rdfs: . - at prefix rdf: . - at prefix owl: . - -acmepubs:citation-search - a moby:Provider, pubs:citationSearch ; - moby:name "AcmePubs Citation Search" ; - moby:oneLineDescription "Industry standard search" ; - moby:operatesOn [ - a rdf:Bag ; - rdf:_1 [ - a moby:Graph ; - moby:hasMapping [ - a moby:Subject, go:GeneSymbol ; - acmeterms:geneSymbol _:bnode1 ; - moby:mapsTo [ - a moby:Object, sgd:LiteratureGuide ; - acmeterms:literatureGuideURI _:bnode2 - ] - ] - ] + at prefix acmepubs: . + at prefix acmeterms: . + at prefix pubs: . + at prefix go: . + at prefix sgd: . + at prefix moby: . + at prefix rdfs: . + at prefix rdf: . + at prefix owl: . + +acmepubs:citation-search + a moby:Provider, pubs:citationSearch ; + moby:name "AcmePubs Citation Search" ; + moby:oneLineDescription "Industry standard search" ; + moby:operatesOn [ + a rdf:Bag ; + rdf:_1 [ + a moby:Graph ; + moby:hasMapping [ + a moby:Subject, go:GeneSymbol ; + acmeterms:geneSymbol _:bnode1 ; + moby:mapsTo [ + a moby:Object, sgd:LiteratureGuide ; + acmeterms:literatureGuideURI _:bnode2 + ] + ] + ] ] . \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf 2004/07/15 20:30:18 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf 2004/07/15 20:58:18 1.2 @@ -1,37 +1,37 @@ - - - - - - - - - - - - - Industry standard search - - AcmePubs Citation Search - - - - - - - - - - - - + + + + + + + + + + + + + Industry standard search + + AcmePubs Citation Search + + + + + + + + + + + + \ No newline at end of file From gss at pub.open-bio.org Thu Jul 15 17:01:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:01:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1II3014182@pub.open-bio.org> gss Thu Jul 15 17:01:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14159/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Removed Files: citationSearch.rdf citationSearch.n3 Log Message: Changed name to citation-search moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.8,NONE citationSearch.n3,1.7,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/citationSearch.rdf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/citationSearch.n3,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 17:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:01:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1gtu014225@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms Modified Files: literatureGuideURI.n3 literatureGuideURI geneSymbol geneSymbol.n3 Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms literatureGuideURI.n3,1.1,1.2 literatureGuideURI,1.1,1.2 geneSymbol,1.1,1.2 geneSymbol.n3,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain sgd:LiteratureGuide ; - rdfs:range xsd:anyURI . \ No newline at end of file + rdfs:range xsd:anyURI . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - \ No newline at end of file + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain go:GeneSymbol ; - rdfs:range xsd:string . \ No newline at end of file + rdfs:range xsd:string . From gss at pub.open-bio.org Thu Jul 15 17:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:01:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1gjA014257@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms Modified Files: literatureGuideURI.n3 geneSymbol geneSymbol.n3 literatureGuideURI Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms literatureGuideURI.n3,1.1,1.2 geneSymbol,1.1,1.2 geneSymbol.n3,1.1,1.2 literatureGuideURI,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain sgd:LiteratureGuide ; - rdfs:range xsd:anyURI . \ No newline at end of file + rdfs:range xsd:anyURI . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - \ No newline at end of file + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain go:GeneSymbol ; - rdfs:range xsd:string . \ No newline at end of file + rdfs:range xsd:string . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + From gss at pub.open-bio.org Thu Jul 15 17:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:01:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1goc014280@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.6,1.7 citationSearch.rdf,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/06/16 18:51:13 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/07/15 21:01:42 1.7 @@ -3,7 +3,7 @@ @prefix pubs: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix rdf: . @prefix owl: . @@ -25,4 +25,4 @@ ] ] ] - ] . \ No newline at end of file + ] . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/06/16 18:51:13 1.7 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/07/15 21:01:42 1.8 @@ -6,16 +6,16 @@ xmlns:go="http://www.go.org:8080/terms/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms/" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:megaterms="http://www.megapubs.com:8080/terms/" > - + - + Cool new search @@ -27,11 +27,11 @@ - + - + From gss at pub.open-bio.org Thu Jul 15 17:02:11 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:02:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2BQ7014323@pub.open-bio.org> gss Thu Jul 15 17:02:11 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14298/S-MOBY/ref-impl/server/WebRoot Modified Files: domains.html Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 20:54:37 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 21:02:11 1.6 @@ -83,7 +83,7 @@ www.megapubs.com/citation-search + "http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch Provider description graph for megapubs.com. The notes regarding the From gss at pub.open-bio.org Thu Jul 15 17:02:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:02:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2dPj014357@pub.open-bio.org> gss Thu Jul 15 17:02:39 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage In directory pub.open-bio.org:/tmp/cvs-serv14328/S-MOBY/ref-impl/queries/engage Modified Files: engage-acmepubs-citationSearch.rdf engage-acmepubs-citationSearch.n3 Log Message: Minor changes moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.rdf,1.2,1.3 engage-acmepubs-citationSearch.n3,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf 2004/06/10 23:27:41 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf 2004/07/15 21:02:39 1.3 @@ -6,35 +6,35 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:pubs="http://www.pubs.org:8081/terms#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - + REV7 - + - + - + - + @@ -48,18 +48,18 @@ Industry standard search http://www.acmepubs.com/about/citationSearch - + AcmePubs Citation Search REV5 - + - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3 2004/06/10 23:27:12 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3 2004/07/15 21:02:39 1.3 @@ -3,7 +3,7 @@ @prefix acmepubs: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix rdf: . @prefix owl: . From gss at pub.open-bio.org Thu Jul 15 17:02:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:02:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2doH014380@pub.open-bio.org> gss Thu Jul 15 17:02:39 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery In directory pub.open-bio.org:/tmp/cvs-serv14328/S-MOBY/ref-impl/queries/discovery Modified Files: query.rdf query.n3 Log Message: Minor changes moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.3,1.4 query.n3,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf 2004/06/18 21:45:07 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf 2004/07/15 21:02:39 1.4 @@ -2,17 +2,17 @@ xmlns:sgd="http://www.sgd.org:8080/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:go="http://www.go.org:8080/terms/" - xmlns:moby="http://www.s-moby.org:8080/terms/" > + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" > - + - + - + @@ -22,6 +22,6 @@ - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3 2004/06/18 21:45:07 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3 2004/07/15 21:02:39 1.4 @@ -1,6 +1,6 @@ @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdf: . _:provider From gss at pub.open-bio.org Mon Jul 19 14:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 19 Jul 2004 14:21:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILat5004196@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/graph Modified Files: MOBYDescriptor.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYDescriptor.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/19 18:21:36 1.2 @@ -2,6 +2,8 @@ import java.net.URI; +import com.hp.hpl.jena.rdf.model.Resource; + /** * The Resource interface represents things that are available * at a URI. @@ -11,5 +13,5 @@ /** * Return the URI represented by this node. */ - public String getURI(); + public Resource getResource(); } From gss at pub.open-bio.org Mon Jul 19 14:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 19 Jul 2004 14:21:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILaer004215@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/parser Modified Files: Parser.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/15 20:28:53 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/19 18:21:36 1.6 @@ -212,8 +212,8 @@ // oneLineDescription, aboutURI, and collection of operatesOn subgraphs // return MOBYObjectFactory.newProvider( - provider.getURI(), name, oneLiner, aboutURI, - MOBYObjectFactory.newUnorderedCollection(null, operatesOn, model), + provider, name, oneLiner, aboutURI, + MOBYObjectFactory.newUnorderedCollection(provider, operatesOn, model), model); } @@ -234,7 +234,7 @@ // hasMapping property that leads to its mapping subgraph. // Resource hasMapping = getResourcePropertyValue(res, MOBY.hasMapping); - return MOBYObjectFactory.newGraph(null, parseHasMapping(hasMapping), model); + return MOBYObjectFactory.newGraph(res, parseHasMapping(hasMapping), model); } else { @@ -318,9 +318,9 @@ // Create and return a Subject to describe this hasMapping subgraph // - return MOBYObjectFactory.newSubject(res.getURI(), - MOBYObjectFactory.newFixedCollection(null, statements, model), - MOBYObjectFactory.newUnorderedCollection(null, directMappings, model), + return MOBYObjectFactory.newSubject(res, + MOBYObjectFactory.newFixedCollection(res, statements, model), + MOBYObjectFactory.newUnorderedCollection(res, directMappings, model), collectionFor(res, nestedMappings), model); } @@ -362,8 +362,8 @@ // Create and return a new MOBYObject // Model model = res.getModel(); - return MOBYObjectFactory.newObject(res.getURI(), - MOBYObjectFactory.newFixedCollection(null, statements, model), + return MOBYObjectFactory.newObject(res, + MOBYObjectFactory.newFixedCollection(res, statements, model), collectionFor(res, nested), model); } @@ -486,13 +486,13 @@ private MOBYCollection collectionFor(Resource res, List elements) { if (isList(res)) { - return MOBYObjectFactory.newFixedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newFixedCollection(res, elements, res.getModel()); } else if (isBag(res)) { - return MOBYObjectFactory.newUnorderedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newUnorderedCollection(res, elements, res.getModel()); } else if (isSeq(res)) { - return MOBYObjectFactory.newOrderedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newOrderedCollection(res, elements, res.getModel()); } else if (isAlt(res)) { - return MOBYObjectFactory.newEnumeration(null, elements, res.getModel()); + return MOBYObjectFactory.newEnumeration(res, elements, res.getModel()); } else { return null; } From gss at pub.open-bio.org Mon Jul 19 14:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 19 Jul 2004 14:21:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILaxW004177@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/graph/impl Modified Files: MOBYProviderImpl.java MOBYFixedCollectionImpl.java MOBYResizableCollectionImpl.java MOBYObjectImpl.java MOBYUnorderedCollectionImpl.java MOBYDocumentImpl.java MOBYGraphImpl.java MOBYMappingElementImpl.java MOBYOrderedCollectionImpl.java MOBYOntologyImpl.java MOBYEnumerationImpl.java MOBYDescriptorImpl.java MOBYCollectionImpl.java MOBYSubjectImpl.java MOBYGraphNodeImpl.java MOBYSingleElementImpl.java MOBYObjectFactory.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderImpl.java,1.1,1.2 MOBYFixedCollectionImpl.java,1.1,1.2 MOBYResizableCollectionImpl.java,1.1,1.2 MOBYObjectImpl.java,1.1,1.2 MOBYUnorderedCollectionImpl.java,1.1,1.2 MOBYDocumentImpl.java,1.1,1.2 MOBYGraphImpl.java,1.1,1.2 MOBYMappingElementImpl.java,1.1,1.2 MOBYOrderedCollectionImpl.java,1.1,1.2 MOBYOntologyImpl.java,1.1,1.2 MOBYEnumerationImpl.java,1.1,1.2 MOBYDescriptorImpl.java,1.1,1.2 MOBYCollectionImpl.java,1.1,1.2 MOBYSubjectImpl.java,1.1,1.2 MOBYGraphNodeImpl.java,1.1,1.2 MOBYSingleElementImpl.java,1.1,1.2 MOBYObjectFactory.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java 2004/07/19 18:21:36 1.2 @@ -16,11 +16,11 @@ private MOBYUnorderedCollection operatesOn; private Model underlying; - MOBYProviderImpl(String uri, String name, String oneLineDescription, + MOBYProviderImpl(Resource resource, String name, String oneLineDescription, String moreInfoURI, MOBYUnorderedCollection operatesOn, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.name = name; this.oneLineDescription = oneLineDescription; this.moreInfoURI = moreInfoURI; =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,16 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYFixedCollectionImpl extends MOBYCollectionImpl implements MOBYFixedCollection { - public MOBYFixedCollectionImpl(String uri, List elements, Model underlying) + public MOBYFixedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isResizable() { return false; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,16 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; abstract class MOBYResizableCollectionImpl extends MOBYCollectionImpl implements MOBYResizableCollection { - MOBYResizableCollectionImpl(String uri, List elements, Model underlying) + MOBYResizableCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isResizable() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java 2004/07/19 18:21:36 1.2 @@ -3,14 +3,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYObjectImpl extends MOBYMappingElementImpl implements MOBYObject { - MOBYObjectImpl(String uri, MOBYFixedCollection statements, + MOBYObjectImpl(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedElements, Model underlying) { - super(uri, statements, nestedElements, underlying); + super(resource, statements, nestedElements, underlying); } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,14 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYUnorderedCollectionImpl extends MOBYResizableCollectionImpl implements MOBYUnorderedCollection { - MOBYUnorderedCollectionImpl(String uri, List elements, Model underlying) + MOBYUnorderedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isOrdered() { return false; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java 2004/07/19 18:21:36 1.2 @@ -8,8 +8,8 @@ extends MOBYDescriptorImpl implements MOBYDocument { - MOBYDocumentImpl(String uri, Model underlying) + MOBYDocumentImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYGraphImpl extends MOBYSingleElementImpl @@ -10,9 +11,9 @@ { private MOBYGraphNode hasMapping; - MOBYGraphImpl(String uri, MOBYGraphNode hasMapping, Model underlying) + MOBYGraphImpl(Resource resource, MOBYGraphNode hasMapping, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.hasMapping = hasMapping; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; public class MOBYMappingElementImpl extends MOBYSingleElementImpl @@ -11,10 +12,10 @@ private MOBYFixedCollection statements; private MOBYCollection nestedElements; - public MOBYMappingElementImpl(String uri, MOBYFixedCollection statements, + public MOBYMappingElementImpl(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedElements, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.statements = statements; this.nestedElements = nestedElements; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYOrderedCollectionImpl extends MOBYResizableCollectionImpl implements MOBYOrderedCollection { - - public MOBYOrderedCollectionImpl(String uri, List elements, Model underlying) + public MOBYOrderedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isOrdered() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java 2004/07/19 18:21:36 1.2 @@ -7,7 +7,7 @@ extends MOBYDocumentImpl implements MOBYOntology { - MOBYOntologyImpl(String uri, Model underlying) { - super(uri, underlying); + MOBYOntologyImpl(Resource resource, Model underlying) { + super(resource, underlying); } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java 2004/07/19 18:21:36 1.2 @@ -10,9 +10,9 @@ extends MOBYUnorderedCollectionImpl implements MOBYEnumeration { - MOBYEnumerationImpl(String uri, List elements, Model underlying) + MOBYEnumerationImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isEnumeration() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java 2004/07/19 18:21:36 1.2 @@ -6,21 +6,26 @@ public abstract class MOBYDescriptorImpl implements MOBYDescriptor { protected Model underlying; - protected String uri; + protected Resource resource; - MOBYDescriptorImpl(String uri, Model underlying) + MOBYDescriptorImpl(Resource resource, Model underlying) { - this.uri = uri; + this.resource = resource; this.underlying = underlying; } - public String getURI() + public Resource getResource() { - return uri; + return resource; } public Model getUnderlying() { return underlying; } + + public String getURI() + { + return (resource == null) ? null : resource.getURI(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -1,9 +1,7 @@ package org.smoby.graph.impl; import org.smoby.graph.*; - -import com.hp.hpl.jena.rdf.model.Model; - +import com.hp.hpl.jena.rdf.model.*; import java.util.*; abstract class MOBYCollectionImpl @@ -12,9 +10,9 @@ { protected List elements = new ArrayList(); - MOBYCollectionImpl(String uri, List elements, Model underlying) + MOBYCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, underlying); + super(resource, underlying); for (Iterator it = elements.iterator(); it.hasNext();) { this.elements.add(it.next()); } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYSubjectImpl extends MOBYMappingElementImpl @@ -10,11 +11,11 @@ { private MOBYUnorderedCollection directMappings; - MOBYSubjectImpl(String uri, MOBYFixedCollection statements, + MOBYSubjectImpl(Resource resource, MOBYFixedCollection statements, MOBYUnorderedCollection directMappings, MOBYCollection nestedMappings, Model underlying) { - super(uri, statements, nestedMappings, underlying); + super(resource, statements, nestedMappings, underlying); this.directMappings = directMappings; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java 2004/07/19 18:21:36 1.2 @@ -1,19 +1,18 @@ package org.smoby.graph.impl; import org.smoby.graph.*; - -import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.*; abstract class MOBYGraphNodeImpl extends MOBYDescriptorImpl implements MOBYGraphNode { - MOBYGraphNodeImpl(String uri, Model underlying) + MOBYGraphNodeImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } public boolean isBlank() { - return getURI() == null; + return (resource == null) || (resource.getURI() == null); } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java 2004/07/19 18:21:36 1.2 @@ -5,14 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYSingleElementImpl extends MOBYGraphNodeImpl implements MOBYSingleElement { - MOBYSingleElementImpl(String uri, Model underlying) + MOBYSingleElementImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } public boolean isSingular() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java 2004/06/18 21:37:52 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java 2004/07/19 18:21:36 1.3 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import org.smoby.graph.impl.*; import com.hp.hpl.jena.rdf.model.*; + import java.util.*; /** @@ -11,32 +12,32 @@ */ public final class MOBYObjectFactory { - public static MOBYFixedCollection newFixedCollection(String uri, List elements, Model underlying) + public static MOBYFixedCollection newFixedCollection(Resource resource, List elements, Model underlying) { - return new MOBYFixedCollectionImpl(uri, elements, underlying); + return new MOBYFixedCollectionImpl(resource, elements, underlying); } - public static MOBYOrderedCollection newOrderedCollection(String uri, List elements, Model underlying) + public static MOBYOrderedCollection newOrderedCollection(Resource resource, List elements, Model underlying) { - return new MOBYOrderedCollectionImpl(uri, elements, underlying); + return new MOBYOrderedCollectionImpl(resource, elements, underlying); } - public static MOBYUnorderedCollection newUnorderedCollection(String uri, List elements, Model underlying) + public static MOBYUnorderedCollection newUnorderedCollection(Resource resource, List elements, Model underlying) { - return new MOBYUnorderedCollectionImpl(uri, elements, underlying); + return new MOBYUnorderedCollectionImpl(resource, elements, underlying); } - public static MOBYEnumeration newEnumeration(String uri, List elements, Model underlying) + public static MOBYEnumeration newEnumeration(Resource resource, List elements, Model underlying) { - return new MOBYEnumerationImpl(uri, elements, underlying); + return new MOBYEnumerationImpl(resource, elements, underlying); } public static MOBYProvider newProvider( - String uri, String name, String oneLineDescription, + Resource resource, String name, String oneLineDescription, String moreInfoURI, MOBYUnorderedCollection operatesOn, Model underlying) { - return new MOBYProviderImpl(uri, name, oneLineDescription, moreInfoURI, operatesOn, + return new MOBYProviderImpl(resource, name, oneLineDescription, moreInfoURI, operatesOn, underlying); } @@ -45,24 +46,24 @@ return new MOBYProviderSetImpl(); } - public static MOBYGraph newGraph(String uri, MOBYGraphNode hasMapping, Model underlying) + public static MOBYGraph newGraph(Resource resource, MOBYGraphNode hasMapping, Model underlying) { - return new MOBYGraphImpl(uri, hasMapping, underlying); + return new MOBYGraphImpl(resource, hasMapping, underlying); } public static MOBYSubject newSubject( - String uri, MOBYFixedCollection statements, + Resource resource, MOBYFixedCollection statements, MOBYUnorderedCollection directMappings, MOBYCollection nestedMappings, Model underlying) { - return new MOBYSubjectImpl(uri, statements, directMappings, + return new MOBYSubjectImpl(resource, statements, directMappings, nestedMappings, underlying); } - public static MOBYObject newObject(String uri, MOBYFixedCollection statements, + public static MOBYObject newObject(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedMappings, Model underlying) { - return new MOBYObjectImpl(uri, statements, nestedMappings, underlying); + return new MOBYObjectImpl(resource, statements, nestedMappings, underlying); } public static MOBYPropertyValueStatement newPropertyValueStatement( From gss at pub.open-bio.org Mon Jul 19 17:22:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 19 Jul 2004 17:22:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407192122.i6JLM94E004903@pub.open-bio.org> gss Mon Jul 19 17:22:09 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv4878/src/org/smoby/vocabulary Modified Files: MOBY.java Log Message: Added keyword property moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/15 20:28:04 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/19 21:22:09 1.6 @@ -36,4 +36,5 @@ public static final Property mapsTo = property(getURI(), "mapsTo"); public static final Property lastModifiedDate = property(getURI(), "lastModifiedDate"); public static final Property Property = property(getURI(), "Property"); + public static final Property keyword = property(getURI(), "keyword"); } \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 17:59:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 17:59:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212159.i6LLxocL012810@pub.open-bio.org> gss Wed Jul 21 17:59:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv12789/S-MOBY/ref-impl/core/src/org/smoby/graph Added Files: MOBYGraphVisitor.java Log Message: Placeholder moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYGraphVisitor.java,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 18:00:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:00:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212200.i6LM0KnH012853@pub.open-bio.org> gss Wed Jul 21 18:00:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv12828/S-MOBY/ref-impl/semanticmoby.org Modified Files: .mymetadata Log Message: Minor changes moby-live/S-MOBY/ref-impl/semanticmoby.org .mymetadata,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata 2004/07/21 22:00:20 1.2 @@ -1,6 +1,7 @@ - + From gss at pub.open-bio.org Wed Jul 21 18:01:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1GA7012884@pub.open-bio.org> gss Wed Jul 21 18:01:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv12860/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Jul 21 18:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JRA012926@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Added Files: cshl-logo.jpg nsf-logo.jpg help1.png ncgr-logo.jpg rdf-logo.PNG Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images cshl-logo.jpg,NONE,1.1 nsf-logo.jpg,NONE,1.1 help1.png,NONE,1.1 ncgr-logo.jpg,NONE,1.1 rdf-logo.PNG,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 18:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JKj012949@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Modified Files: KeywordSearchServlet.java BaseServlet.java Added Files: ProviderEngagementServlet.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets ProviderEngagementServlet.java,NONE,1.1 KeywordSearchServlet.java,1.1,1.2 BaseServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:01:19 1.2 @@ -1,10 +1,11 @@ package org.smoby.ref.servlets; import java.io.*; - +import java.util.*; import javax.servlet.*; import javax.servlet.http.*; -import javax.servlet.http.HttpServletResponse; +import org.smoby.graph.*; +import org.smoby.ref.tools.*; public class KeywordSearchServlet extends BaseServlet { @@ -12,37 +13,121 @@ throws ServletException, IOException { PrintStream out = new PrintStream(response.getOutputStream()); + + List provider = getKeywords("provider", request); + List accepts = getKeywords("accepts", request); + List returns = getKeywords("returns", request); + startHTML(response, out); + if ((provider == null) && (accepts == null) && (returns == null)) + { + showResultCount(-1, out); + } + else + { + KeywordQuery q = new KeywordQuery(provider, accepts, returns); + + List matching = q.findMatchingProviders(); + + showResultCount(matching.size(), out); + + for (Iterator it = matching.iterator(); it.hasNext();) + { + MOBYProvider p = (MOBYProvider) it.next(); + showProvider(p, out); + } + } finishHTML(response, out); } - private void startHTML(HttpServletResponse response, PrintStream out) + private List getKeywords(String paramName, HttpServletRequest request) { - response.setContentType("text/html"); - out.println(""); - out.println(""); - out.println("Semantic MOBY search results"); - out.println(""); - out.println("

"); - out.println("Semantic"); - out.println("M" + - "OBY"); - out.println("

"); + List keywords = new ArrayList(); + + String value = request.getParameter(paramName); + if (value == null) return keywords; + + value = value.trim(); + + if (value.length() == 0) return keywords; + + StreamTokenizer st = new StreamTokenizer(new StringReader(value)); + st.wordChars('*', '*'); + st.wordChars('%', '%'); + try + { + while (st.nextToken() != StreamTokenizer.TT_EOF) + { + if (st.sval != null) + { + String val = st.sval.toLowerCase().trim().replace('*', '%'); + keywords.add(val); + } + } + } catch (IOException e) {} + + return keywords; } private void showResultCount(int count, PrintStream out) { - if (count < 1) { - out.println("No matches"); + out.println(""); + out.println(""); + out.println(""); + out.println(""); + out.println("
"); + + if (count < 0) { + out.println("No keywords were entered, so no search was performed."); + } else if (count < 1) { + out.println("No matching providers were found. Note that"); + out.println("very few providers have yet been defined."); } else { - out.println("" + count + " results found:"); + out.println(count + " matching provider" + + (count > 1 ? "s" : "") + " found"); } + out.println("
"); + out.println("
"); } - private void finishHTML(HttpServletResponse response, PrintStream out) + private void showProvider(MOBYProvider provider, PrintStream out) { - response.setContentType("text/html"); - out.println(""); + String uri = provider.getResource().getURI(); + String name = provider.getName(); + String description = provider.getOneLineDescription(); + String moreInfo = provider.getMoreInfoURI(); + + out.println(""); + out.print(""); + if ((name != null) && (name.trim().length() > 0)) { + out.println(name); + } else { + out.println(uri); + } + out.print(""); + out.println(""); + out.print(""); + out.print("\"Definition\""); + out.print(""); + out.println("
"); + + if ((description != null) && (description.trim().length() > 0)) { + out.println(description); + } else { + out.println("No description is available for this provider."); + } + out.println("
"); + + if ((moreInfo != null) && (moreInfo.trim().length() > 0)) { + out.println("For more information see " + moreInfo + ""); + } + out.println("
"); } public void doPost(HttpServletRequest request, HttpServletResponse response) =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java 2004/07/21 22:01:19 1.2 @@ -5,6 +5,7 @@ import javax.servlet.*; import javax.servlet.http.*; + import org.smoby.ref.tools.*; import org.smoby.servlet.*; import org.apache.log4j.*; @@ -48,4 +49,32 @@ } } } + + protected void startHTML(HttpServletResponse response, PrintStream out) + { + response.setContentType("text/html"); + out.println(""); + out.println(""); + out.println("Semantic MOBY search results"); + out.println(""); + out.println("
"); + out.println("

"); + out.println(""); + out.println("Semantic"); + out.println("M" + + "OBY" + + ""); + out.println(""); + out.println("

"); + out.println("
"); + out.println(""); + out.println(""); + } + + protected void finishHTML(HttpServletResponse response, PrintStream out) + { + out.println(""); + out.println(""); + out.println(""); + } } \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 18:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JDv012969@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Modified Files: HelloWorldServlet.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/15 20:27:16 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/21 22:01:19 1.2 @@ -4,6 +4,7 @@ import java.util.*; import javax.servlet.*; import javax.servlet.http.*; + import org.smoby.graph.*; import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.ref.servlets.*; @@ -48,4 +49,12 @@ // Silently ignore graphs without the required form catch (Throwable t) {} } + + /** + * Return the last modification date of the description graph file + */ + public long getLastModified(HttpServletRequest request) + { + return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); + } } From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KvG013015@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot Modified Files: help.html index.html Added Files: .cvsignore Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot .cvsignore,NONE,1.1 help.html,1.1,1.2 index.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:01:20 1.2 @@ -1,26 +1,56 @@ -Semantic MOBY Help +Semantic MOBY Search Help

Semantic MOBY -Help +Search Help

-
-

+ Semantic MOBY maintains a searchable repository of descriptions of -providers of services that are available on the web. At the heart -of these descriptions is the notion of mapping, that a provider -"accepts" one type of thing, maps it to another thing that it returns -as a result. For example, entering -the following terms is asking Semantic MOBY to search its repository -for providers that accept terms described as "gene symbols" and return -things whose descriptions match the wildcard pattern "publication*". +providers of services that are available on the web. At the heart +of these descriptions is the notion that providers map one type +of thing (what the provider accepts) to another type of thing (what +the provider returns). +

+Providers, as well as things accepted and returned by providers, are +classified using web-accessible descriptions, and these descriptions +have keywords associated with them. For example, the following shows +a query for providers whose descriptions include the keyword "hello":

-. +.
+
+Search hints +
    +
  • Keywords are not case sensitive, so HELLO means the +same thing as hello as does HeLloW. +

    +
  • The wildcard character (*) can be used at the end of a keyword +to match keywords that start with the characters before the wildcard. +For example, he* will match hello as well +as help. +

    +
  • Multiple words enclosed in double quotes are considered to be a +single keyword. For example, the quoted string "gene symbol" +is considered to be a single keyword composed of 11 characters, including a space. +The wildcard character is interpreted literally (i.e. as the '*' +character) if it appears within a quoted string. +

    +
  • Multiple keywords may be typed in one of the fields; this means to +search for any of the keywords in that field. For example, +typing fat sugar in the accepts field will search for +providers that map either fat or sugar to something else. +

    +
  • If keywords are typed in multiple fields, then only providers that +match keywords for all the fields will match. For example, +typing fat sugar into the accepts field, and +"weight gain" into the returns field will search for +providers that map either fat or sugar to weight gain. +

    +
=================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:01:20 1.2 @@ -16,21 +16,45 @@ Accepts Returns - - - + + +
Type any terms into the boxes above and press Search
-(for example type Hello into the Provider box) +(for example type 'hello' (without quotes) into the Provider box)

-

About Semantic MOBY   Help on Searching +


+ + + + + + + + + + + +
+ + CSHL + + NCGR + + NSF
+ + Cold Spring Harbor Laboratory + + National Center for Genome Resources + + National Science Foundation
From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KM9013059@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Modified Files: hello-world.n3 hello-world.rdf Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello hello-world.n3,1.1,1.2 hello-world.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3 2004/07/21 22:01:20 1.2 @@ -7,7 +7,7 @@ @prefix xsd: . ex:hello-world - a moby:Provider ; + a moby:Provider, exterms:GreetingProvider ; moby:name "Semantic MOBY Hello World provider" ; moby:oneLineDescription "Simple example of a Semantic MOBY provider" ; moby:operatesOn [ =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf 2004/07/21 22:01:20 1.2 @@ -8,20 +8,21 @@ xmlns:moby="http://www.semanticmoby.org/ontologies/core/" > + Simple example of a Semantic MOBY provider Semantic MOBY Hello World provider - - - - - + - + + + + + \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1Kfw012988@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Modified Files: URIInvestigator.java Added Files: KeywordQuery.java KeywordList.java KeywordFinder.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools KeywordQuery.java,NONE,1.1 KeywordList.java,NONE,1.1 KeywordFinder.java,NONE,1.1 URIInvestigator.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java 2004/07/15 20:27:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java 2004/07/21 22:01:19 1.2 @@ -216,7 +216,8 @@ // retrievable, but register the graph anyway // syncLog.warn("Unable to get Last-Modified date for " - + providerURI + "; ignoring"); + + providerURI + "; using current date"); + lastModifiedDate = new Date(); } catch (Throwable t) { From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1Knv013083@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageManager.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/21 22:01:20 1.2 @@ -9,6 +9,8 @@ import com.hp.hpl.jena.rdf.model.*; import com.hp.hpl.jena.shared.*; import com.hp.hpl.jena.vocabulary.*; +import java.sql.Connection; +import java.sql.SQLException; import java.util.*; /** @@ -60,7 +62,7 @@ { Model model = ((MOBYProviderImpl) provider).getUnderlying(); Model dbModel = null; - String uriString = provider.getURI(); + String uriString = provider.getResource().getURI(); Resource uri = model.createResource(uriString); try @@ -100,6 +102,12 @@ dbModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime()); } + // Add keywords associated with the provider + // + KeywordFinder finder = new KeywordFinder(provider, model); + addKeywords(provider.getResource().getURI(), + finder.getKeywords(), dbModel); + // Commit the transaction on the database model // dbModel.commit(); @@ -116,6 +124,73 @@ } } } + + private void addKeywords(String providerURI, KeywordList list, Model model) + throws StorageException + { + try + { + ModelRDB dbModel = (ModelRDB) model; + Connection conn = dbModel.getConnection().getConnection(); + + java.sql.Statement sql = conn.createStatement(); + + doAddKeywords(providerURI, list.getProviderKeywords(), "P", sql); + doAddKeywords(providerURI, list.getSubjectKeywords(), "S", sql); + doAddKeywords(providerURI, list.getObjectKeywords(), "O", sql); + + } + catch (Throwable t) + { + throw new StorageException(t); + } + } + + private void doAddKeywords(String providerURI, Iterator it, + String appliesTo, java.sql.Statement sql) + throws SQLException + { + while (it.hasNext()) + { + String keyword = it.next().toString(); + + StringBuffer sb = new StringBuffer(); + + sb.append("INSERT INTO MOBY_KEYWORD\n"); + sb.append(" (keyword, provider_uri, applies_to)\n"); + sb.append("values ('"); + sb.append(keyword.toLowerCase().trim()); + sb.append("', '"); + sb.append(providerURI); + sb.append("', '"); + sb.append(appliesTo); + sb.append("')"); + + String queryString = sb.toString(); + + sql.execute(queryString); + } + } + + private void removeKeywords(String providerURI, Model model) + throws StorageException + { + try + { + ModelRDB dbModel = (ModelRDB) model; + Connection conn = dbModel.getConnection().getConnection(); + + java.sql.Statement sql = conn.createStatement(); + + sql.execute("DELETE FROM MOBY_KEYWORD WHERE provider_uri = '" + + providerURI + "'"); + + } + catch (Throwable t) + { + throw new StorageException(t); + } + } /** * Remove all the statements registered by a given provider URI @@ -143,6 +218,10 @@ // ProviderRemover.remove(dbModel, providerURI); + // Remove keywords associated with the provider URI + // + removeKeywords(providerURI, dbModel); + // Commit the transaction on the database // dbModel.commit(); From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KH3013030@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Added Files: GreetingProvider.n3 GreetingProvider index.html Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies GreetingProvider.n3,NONE,1.1 GreetingProvider,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 18:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KKL013102@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Modified Files: web.xml Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml 2004/07/21 22:01:20 1.2 @@ -17,6 +17,13 @@ + ProviderEngagementServlet + engage-provider + Keyword search servlet + org.smoby.ref.servlets.ProviderEngagementServlet + + + HelloWorldServlet hello-world Hello World simple application @@ -64,6 +71,11 @@ + ProviderEngagementServlet + /engage-provider + + + HelloWorldServlet /examples/hello-world From gss at pub.open-bio.org Wed Jul 21 18:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:35:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZP58013212@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Modified Files: help1.png Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images help1.png,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png 2004/07/21 22:01:19 1.1 and /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png 2004/07/21 22:35:25 1.2 differ rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png: diff failed From gss at pub.open-bio.org Wed Jul 21 18:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:35:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZP6f013240@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/WebRoot Modified Files: help.html tech-overview.html index.html Removed Files: help1.jpg Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot help.html,1.2,1.3 tech-overview.html,1.1,1.2 index.html,1.2,1.3 help1.jpg,1.1,NONE =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:35:25 1.3 @@ -13,13 +13,13 @@ Semantic MOBY maintains a searchable repository of descriptions of providers of services that are available on the web. At the heart of these descriptions is the notion that providers map one type -of thing (what the provider accepts) to another type of thing (what -the provider returns). +of thing (the Subject) to another (the Object), or +vice versa.

-Providers, as well as things accepted and returned by providers, are -classified using web-accessible descriptions, and these descriptions +Providers, as well as subjects and objects, are +classified using web-accessible definitions (ontologies), and these definitions have keywords associated with them. For example, the following shows -a query for providers whose descriptions include the keyword "hello": +a query for providers whose definitions include the keyword "hello":

. @@ -28,7 +28,7 @@ Search hints
  • Keywords are not case sensitive, so HELLO means the -same thing as hello as does HeLloW. +same thing as hello as does HeLlO.

  • The wildcard character (*) can be used at the end of a keyword to match keywords that start with the characters before the wildcard. @@ -43,13 +43,13 @@

  • Multiple keywords may be typed in one of the fields; this means to search for any of the keywords in that field. For example, -typing fat sugar in the accepts field will search for +typing fat sugar in the Subject field will search for providers that map either fat or sugar to something else.

  • If keywords are typed in multiple fields, then only providers that match keywords for all the fields will match. For example, -typing fat sugar into the accepts field, and -"weight gain" into the returns field will search for +typing fat sugar into the Subject field, and +"weight gain" into the Object field will search for providers that map either fat or sugar to weight gain.

=================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html 2004/07/21 22:35:25 1.2 @@ -34,7 +34,11 @@ a Semantic MOBY provider, and should be examined first. -Graph
converter + + +Graph
converter + + An example that converts among various formats of OWL graphs. =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:35:25 1.3 @@ -13,8 +13,8 @@ - - + + @@ -45,15 +45,20 @@ NSF + CSHL + NCGR + NSF + + +
ProviderAcceptsReturns
SubjectObject
- - Cold Spring Harbor Laboratory - - National Center for Genome Resources - - National Science Foundation
+
+
+ +
+Under Construction - Pardon the Dust
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/help1.jpg,v: No such file or directory From gss at pub.open-bio.org Wed Jul 21 18:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:35:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZPGs013260@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Modified Files: KeywordSearchServlet.java Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets KeywordSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:01:19 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:35:25 1.3 @@ -19,7 +19,7 @@ List returns = getKeywords("returns", request); startHTML(response, out); - if ((provider == null) && (accepts == null) && (returns == null)) + if ((provider.isEmpty()) && (accepts.isEmpty()) && (returns.isEmpty())) { showResultCount(-1, out); } From mwilkinson at pub.open-bio.org Mon Jul 26 13:09:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 26 Jul 2004 13:09:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407261709.i6QH99FA005183@pub.open-bio.org> mwilkinson Mon Jul 26 13:09:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv5164/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: fixed a nasty bug that was preventing the proper registration of collection output services moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/09 00:21:53 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/26 17:09:09 1.3 @@ -102,23 +102,23 @@ sub insert_collection_input { my ($self, %args) = @_; my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ +# if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ # this should be dropped down into the mysql.pm module?? probably... $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); my $id=$self->dbh->{mysql_insertid}; return $id; - } +# } } sub insert_collection_output { my ($self, %args) = @_; my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ +# if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ # this should be dropped down into the mysql.pm module?? probably... $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); my $id=$self->dbh->{mysql_insertid}; return $id; - } +# } } sub insert_simple_input { From mwilkinson at pub.open-bio.org Tue Jul 27 18:56:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 27 Jul 2004 18:56:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407272256.i6RMuXo3012522@pub.open-bio.org> mwilkinson Tue Jul 27 18:56:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv12503/MOBY/Client Modified Files: CollectionArticle.pm Log Message: simples were being added to collections multiple times when creating a ServiceInstance from a DOM, rather than from parsing the XML manually. Fixed. RDF should now be somewhat more sensible. moby-live/Perl/MOBY/Client CollectionArticle.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/06/15 00:37:55 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/07/27 22:56:32 1.9 @@ -306,10 +306,7 @@ $self->articleName($articleName); my $objects = $dom->getElementsByTagName("Simple"); for my $n(0..$objects->getLength - 1){ - foreach my $child($objects->item($n)->getChildNodes){ - next unless $child->getNodeType == ELEMENT_NODE; - $self->addSimple(MOBY::Client::SimpleArticle->new(articleName=>$self->articleName, XML_DOM => $objects->item($n))); - } + $self->addSimple(MOBY::Client::SimpleArticle->new(articleName=>$self->articleName, XML_DOM => $objects->item($n))); } return $self; } From mwilkinson at pub.open-bio.org Wed Jul 28 18:55:14 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 18:55:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282255.i6SMtEH9016063@pub.open-bio.org> mwilkinson Wed Jul 28 18:55:13 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16045/RDF Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/RDF added to the repository moby-live/Perl/MOBY/RDF - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Wed Jul 28 18:56:59 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 18:56:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282256.i6SMuxUG016129@pub.open-bio.org> mwilkinson Wed Jul 28 18:56:59 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16114/RDF Added Files: ServiceInstanceRDF.pm InOutArticlesRDF.pm Log Message: added two new modules for generating RDF of MOBY-S Service Instances. This serves both the straight URL RDF documents, as well as (in a few minutes) the LSID metadata resolver service moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,NONE,1.1 InOutArticlesRDF.pm,NONE,1.1 From mwilkinson at pub.open-bio.org Wed Jul 28 18:59:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 18:59:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282259.i6SMxYGc016201@pub.open-bio.org> mwilkinson Wed Jul 28 18:59:34 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16178/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: clean up and add one more test moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.1,1.2 ServiceInstanceRDF.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:56:59 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:59:34 1.2 @@ -47,6 +47,7 @@ return 0 unless $args{'type'} && ( ($args{'type'} =~ /consumes/i) || ($args{'type'} =~ /produces/i) ); return 0 unless $args{'subject'} && (ref($args{'subject'}) =~ /rdf::core/i); return 0 unless $args{'araticles'} && (ref($args{'articles'}) =~ /array/i); + return 1 unless ${$args{'articles'}}[0]; # if there ARE no articles, this is a valid result! my $caller_is_obj = ref($caller); my $class = $caller_is_obj || $caller; @@ -134,13 +135,7 @@ my $namespaces = $ART->namespaces(); foreach (@{$namespaces}){ - # prime with base Object type "Class" - my $namespace = _addClassResource($model, NS, "$_", ''); - #my $type = $subject->new(RDF_NS,'type'); - #my $class = new RDF::Core::Resource(RDFS_NS,'Class'); - #my $statement = new RDF::Core::Statement($namespace, $type, $class); - #$model->addStmt($statement); - + my $namespace = _addClassResource($model, NS, "$_", ''); my $inNamespace = $article->new(MP, 'namespace_type'); my $statement = new RDF::Core::Statement($article, $inNamespace, $namespace); $model->addStmt($statement); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:56:59 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:59:34 1.2 @@ -69,16 +69,9 @@ _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title my $inputs = $service->input; - #my @inputs = @{$inputs}; my $outputs = $service->output; - #my @outputs = @{$outputs}; - -# THERE SHOULD BE A LOOP HERE TO TEST IF ANY INPUTS AT ALL - - - #foreach my $IN(@inputs){ my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', @@ -86,9 +79,6 @@ articles => $inputs, ); - #} -##################################################### - my $OutputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'produces', From mwilkinson at pub.open-bio.org Wed Jul 28 19:00:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:00:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282300.i6SN09fA016280@pub.open-bio.org> mwilkinson Wed Jul 28 19:00:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv16257 Modified Files: INSTALL MANIFEST Log Message: adding new modules to the manifest. removing old outdated installation documents moby-live/Perl INSTALL,1.1,1.2 MANIFEST,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/INSTALL 2003/06/10 17:12:52 1.1 +++ /home/repository/moby/moby-live/Perl/INSTALL 2004/07/28 23:00:09 1.2 @@ -1,33 +1,15 @@ ----------- CLIENT CONFIGURATION ---------- -If you wish to conect, by default, to anything other than -the MOBY Central registry running at the Canadian -Bioinformatics Resource (mobycentral.cbr.nrc.ca) then -you should set the following environment variables: +perl Makefile.PL +make +make install -MOBY_SERVER=http://your.favorite.server/cgi-bin/serverscriptname.pl -MOBY_URI=http://your.favorite.server/PathTo/MOBY -for example, to connect by default to a local copy of -the registry it might look like this: +MOST PEOPLE CAN STOP READING NOW! -MOBY_SERVER=http://localhost/cgi-bin/MOBY-Central.pl -MOBY_URI=http://localhost/MOBY/Central -=========================================== +For details on how to configure your own MOBY Central +registry, should you want to set one up (you DO NOT +need to set up a registry to acess nor service MOBY-S +Services) please visit the "Installing a Local Registy" +link on the biomoby.org homepage. -------- SERVER CONFIGURATION ------------ -If you are installing a local copy of MOBY Central -you will need to set some additional environment -variables in your httpd.conf file to tell the modules -where your mysql installation is. These are -configured using the apache SetEnv directive as follows: - -SetEnv MOBY_CENTRAL_DBNAME mobycentral -SetEnv MOBY_CENTRAL_DBPASS yourpassword -SetEnv MOBY_CENTRAL_DBPORT 3306 -SetEnv MOBY_CENTRAL_DBUSER mobyusername -SetEnv MOBY_CENTRAL_URL localhost - -(don't forget to restart your server...) -========================================== - +Mark =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MANIFEST 2004/06/24 22:32:38 1.11 +++ /home/repository/moby/moby-live/Perl/MANIFEST 2004/07/28 23:00:09 1.12 @@ -45,3 +45,5 @@ MOBY/lsid/authority/RelationshipResolver.pm MOBY/lsid/authority/ServiceInstanceResolver.pm MOBY/lsid/authority/ServiceResolver.pm +MOBY/RDF/ServiceInstanceRDF.pm +MOBY/RDF/InOutArticlesRDF.pm From mwilkinson at pub.open-bio.org Wed Jul 28 19:08:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:08:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282308.i6SN89Nu016375@pub.open-bio.org> mwilkinson Wed Jul 28 19:08:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16356/RDF Modified Files: ServiceInstanceRDF.pm Log Message: RDF/ServiceInstanceRDF.pm moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:59:34 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:08:09 1.3 @@ -1,6 +1,5 @@ package MOBY::RDF::ServiceInstanceRDF; use strict; -use lib '../../'; use MOBY::RDF::InOutArticlesRDF; require Exporter; our @ISA = qw(Exporter); @@ -50,7 +49,7 @@ sub build { my ($self) = @_; - my $service = $self->service; + my $service = $self->service_instance; my $model = $self->model; my $Bag = new RDF::Core::Resource(RDF_NS,'Bag'); From mwilkinson at pub.open-bio.org Wed Jul 28 19:12:11 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:12:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282312.i6SNCBj7016462@pub.open-bio.org> mwilkinson Wed Jul 28 19:12:11 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16439/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: shuffling subroutines around moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.2,1.3 ServiceInstanceRDF.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:59:34 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:12:11 1.3 @@ -141,4 +141,59 @@ $model->addStmt($statement); } } + + + +sub _addResource { + my ($model, $ns, $predicate, $subject, $ons, $object) = @_; + + $predicate = $subject->new($ns, $predicate); + $object = new RDF::Core::Resource($ons, $object); + my $statement = new RDF::Core::Statement($subject, $predicate, $object); + $model->addStmt($statement); + +} + + +# these should also be stripped out into their own module +sub _addClassResource { + my ($model, $ns, $thing, $def) = @_; + my ($subject, $statement, $class, $label, $type); + + $label = ($thing =~ /urn:lsid.*:(\S+)$/)?$1:$thing; + + unless (ref($thing) =~ /RDF/){ + $subject = new RDF::Core::Resource($ns, $thing); + } + + $type = $subject->new(RDF_NS,'type'); + $class = new RDF::Core::Resource(RDFS_NS,'Class'); + $statement = new RDF::Core::Statement($subject, $type, $class); + $model->addStmt($statement); + + $type = $subject->new(RDFS_NS,'label'); + $label = new RDF::Core::Literal($label,"en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject unless $def; + + $type = $subject->new(RDFS_NS,'comment'); + $label = new RDF::Core::Literal($def, "en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject; +} + +sub _addClassLiteral { + my ($model, $pns, $subject, $predicate, $value) = @_; + + $predicate = $subject->new($pns, $predicate); + $value = new RDF::Core::Literal($value, "en", "http://www.w3.org/2001/XMLSchema#string"); + my $statement = new RDF::Core::Statement($subject, $predicate, $value); + $model->addStmt($statement); + +} + 1; \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:08:09 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:12:11 1.4 @@ -88,4 +88,55 @@ } +# these should be stripped out into their own module... +sub _addResource { + my ($model, $ns, $predicate, $subject, $ons, $object) = @_; + + $predicate = $subject->new($ns, $predicate); + $object = new RDF::Core::Resource($ons, $object); + my $statement = new RDF::Core::Statement($subject, $predicate, $object); + $model->addStmt($statement); + +} + +sub _addClassResource { + my ($model, $ns, $thing, $def) = @_; + my ($subject, $statement, $class, $label, $type); + + $label = ($thing =~ /urn:lsid.*:(\S+)$/)?$1:$thing; + + unless (ref($thing) =~ /RDF/){ + $subject = new RDF::Core::Resource($ns, $thing); + } + + $type = $subject->new(RDF_NS,'type'); + $class = new RDF::Core::Resource(RDFS_NS,'Class'); + $statement = new RDF::Core::Statement($subject, $type, $class); + $model->addStmt($statement); + + $type = $subject->new(RDFS_NS,'label'); + $label = new RDF::Core::Literal($label,"en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject unless $def; + + $type = $subject->new(RDFS_NS,'comment'); + $label = new RDF::Core::Literal($def, "en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject; +} + +sub _addClassLiteral { + my ($model, $pns, $subject, $predicate, $value) = @_; + + $predicate = $subject->new($pns, $predicate); + $value = new RDF::Core::Literal($value, "en", "http://www.w3.org/2001/XMLSchema#string"); + my $statement = new RDF::Core::Statement($subject, $predicate, $value); + $model->addStmt($statement); + +} + 1; \ No newline at end of file From mwilkinson at pub.open-bio.org Wed Jul 28 19:41:39 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:41:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282341.i6SNfdka016576@pub.open-bio.org> mwilkinson Wed Jul 28 19:41:39 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16557/RDF Modified Files: InOutArticlesRDF.pm Log Message: adding a class variable counter for the various node factories so that all inputs in the database don't end up getting added to a single service in the RDF >>grin<< moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:12:11 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:41:39 1.4 @@ -1,6 +1,7 @@ package MOBY::RDF::InOutArticlesRDF; use strict; use RDF::Core::NodeFactory; +use RDF::Core::Statement; require Exporter; our @ISA = qw(Exporter); @@ -14,6 +15,35 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +{ + my $inputcounter = 1; + my $outputcounter = 1; + my $simplecounter = 1; + my $collectioncounter = 1; + + sub nextinput { + ++$inputcounter; + $inputcounter = 1 if $inputcounter==100000; + return $inputcounter; + } + sub nextoutput { + ++$outputcounter; + $outputcounter = 1 if $outputcounter==100000; + return $outputcounter; + } + sub nextsimple { + ++$simplecounter; + $simplecounter = 1 if $simplecounter==100000; + return $simplecounter; + } + sub nextcollection { + ++$collectioncounter; + $collectioncounter = 1 if $collectioncounter==100000; + return $collectioncounter; + } + +} + sub type { my ($self, @args) = @_; $args[0] && ($self->{type} = $args[0]); @@ -46,7 +76,7 @@ return 0 unless $args{'model'} && (ref($args{'model'}) =~ /rdf::core/i); return 0 unless $args{'type'} && ( ($args{'type'} =~ /consumes/i) || ($args{'type'} =~ /produces/i) ); return 0 unless $args{'subject'} && (ref($args{'subject'}) =~ /rdf::core/i); - return 0 unless $args{'araticles'} && (ref($args{'articles'}) =~ /array/i); + return 0 unless $args{'articles'} && (ref($args{'articles'}) =~ /array/i); return 1 unless ${$args{'articles'}}[0]; # if there ARE no articles, this is a valid result! my $caller_is_obj = ref($caller); @@ -61,10 +91,10 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &inputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &outputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &simplecounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &collectioncounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); @@ -91,8 +121,9 @@ my @articles = $self->articles; my $Bag = $self->{Bag}; - my $li = 1; + my $li = 0; foreach my $IN(@articles){ + ++$li; my $LI = $Thingy->new(RDF_NS, "_$li"); my $input = $self->{inputfactory}->newResource; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); @@ -111,9 +142,10 @@ _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; my $simps = $IN->Simples; + my $lli=0; foreach my $simp(@{$simps}){ - my $li = 1; - my $LI = $input->new(RDF_NS, "_$li"); + ++$lli; + my $LI = $input->new(RDF_NS, "_$lli"); my $collection_member = $self->{inputfactory}->newResource; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); From mwilkinson at pub.open-bio.org Wed Jul 28 19:45:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:45:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282345.i6SNjXjY016644@pub.open-bio.org> mwilkinson Wed Jul 28 19:45:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16625/RDF Modified Files: InOutArticlesRDF.pm Log Message: call the method, not the variable moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:41:39 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:45:33 1.5 @@ -91,10 +91,10 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &inputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &outputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &simplecounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &collectioncounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &nextinput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &nextoutput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &nextsimple(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &nextcollection(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); From mwilkinson at pub.open-bio.org Wed Jul 28 20:22:21 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 20:22:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407290022.i6T0MLaF016803@pub.open-bio.org> mwilkinson Wed Jul 28 20:22:21 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16780/MOBY/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: ups. Got my class variables wrong. Now it increments properly to associate inputs with the correct services moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.5,1.6 ServiceInstanceRDF.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:45:33 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 00:22:21 1.6 @@ -16,30 +16,22 @@ use constant DC => 'http://purl.org/dc/elements/1.1/'; { - my $inputcounter = 1; - my $outputcounter = 1; - my $simplecounter = 1; - my $collectioncounter = 1; + my $inputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $outputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $simplefactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $collectionfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); sub nextinput { - ++$inputcounter; - $inputcounter = 1 if $inputcounter==100000; - return $inputcounter; + return $inputfactory->newResource } sub nextoutput { - ++$outputcounter; - $outputcounter = 1 if $outputcounter==100000; - return $outputcounter; + return $outputfactory->newResource } sub nextsimple { - ++$simplecounter; - $simplecounter = 1 if $simplecounter==100000; - return $simplecounter; + return $simplefactory->newResource } sub nextcollection { - ++$collectioncounter; - $collectioncounter = 1 if $collectioncounter==100000; - return $collectioncounter; + return $collectionfactory->newResource } } @@ -91,14 +83,14 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &nextinput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &nextoutput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &nextsimple(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &nextcollection(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); - - my $Thingy = $self->{inputfactory}->newResource; # create a bnode + my $Thingy; + if ($self->type eq 'consumes'){ + $Thingy = &nextinput; # create a bnode + } else { + $Thingy = &nextoutput; # create a bnode + } my $predicate = $subject->new(MP,$self->type); # 'consumes' or 'produces' my $statement = new RDF::Core::Statement($subject, $predicate, $Thingy); $model->addStmt($statement); @@ -125,13 +117,12 @@ foreach my $IN(@articles){ ++$li; my $LI = $Thingy->new(RDF_NS, "_$li"); - my $input = $self->{inputfactory}->newResource; + my $input = &nextsimple; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); $model->addStmt($statement); # # - - + if ($IN->isSimple){ &_addSimple($model, $input, $IN); } else { # COLLECTION @@ -146,7 +137,7 @@ foreach my $simp(@{$simps}){ ++$lli; my $LI = $input->new(RDF_NS, "_$lli"); - my $collection_member = $self->{inputfactory}->newResource; + my $collection_member = &nextcollection; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:12:11 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 00:22:21 1.5 @@ -1,6 +1,8 @@ package MOBY::RDF::ServiceInstanceRDF; use strict; use MOBY::RDF::InOutArticlesRDF; +use RDF::Core::Statement; + require Exporter; our @ISA = qw(Exporter); our @EXPORT_OK = qw(); From mwilkinson at pub.open-bio.org Wed Jul 28 20:36:55 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 20:36:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407290036.i6T0atVS016900@pub.open-bio.org> mwilkinson Wed Jul 28 20:36:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv16881/MOBY/lsid/authority Modified Files: ServiceInstanceResolver.pm Log Message: the LSID resolver for service instance LSID's now uses the same modules as the RESOURCES script, and should output identically formatted RDF moby-live/Perl/MOBY/lsid/authority ServiceInstanceResolver.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm 2004/01/15 20:59:38 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm 2004/07/29 00:36:54 1.4 @@ -5,6 +5,35 @@ use XML::DOM; use MOBY::lsid::authority::RDFConfigure qw(:all); use MOBY::Client::Central; +use MOBY::RDF::ServiceInstanceRDF; + +use RDF::Core; +use RDF::Core::Model; +use RDF::Core::Literal; +use RDF::Core::Statement; +use RDF::Core::Model::Serializer; +use RDF::Core::Storage::Memory; +use RDF::Core::Constants qw(:xml :rdf :rdfs); +use constant OBJ => 'http://biomoby.org/RESOURCES/MOBY-S/Objects#'; +use constant SRV => 'http://biomoby.org/RESOURCES/MOBY-S/Services#'; +use constant NS => 'http://biomoby.org/RESOURCES/MOBY-S/Namespaces#'; +use constant MP => 'http://biomoby.org/RESOURCES/MOBY-S/Predicates#'; +use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; +use constant DC => 'http://purl.org/dc/elements/1.1/'; + +sub xmlNamespaces { + return { + RDF_NS() => 'rdf', + RDFS_NS() => 'rdfs', + OBJ() => 'mobyObject', + NS() => 'mobyNamespace', + SRV() => 'mobyService', + MP() => 'mobyPred', + SI() => 'serviceInstances', + DC() => 'dc', + } +} + @ISA = qw(Exporter); @EXPORT_OK = qw( @@ -14,8 +43,21 @@ resolve_ServiceInstance )]); +sub _serialize { + my ($model) = @_; + my $xml = ''; + + my $serializer = new RDF::Core::Model::Serializer( + Model=>$model, + Output=>\$xml, + getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! + ); + $serializer->serialize; + print "$xml\n"; +} sub resolve_ServiceInstance { + my ($ls) = @_; my $lsid= LS::ID->new($ls)->canonical; unless ($lsid) { @@ -37,175 +79,20 @@ unless ($si && ${$si}[0]){ _die('UNKNOWN_LSID'); } - my $service = shift(@{$si}); - # LSID is now fully validated. Carry on with metadata. - $RDF_PREFIX?1:1; - $mdata= $RDF_PREFIX; - - $mdata.= rdfLiteral( - $lsid->as_string, - 'rdf:type', # rdf:Type - 'i3csp:bioMobyService' - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:name', # i3c:Name - $service->name - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:title', # dc:Title - $service->name - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:label', # dc:Label - $service->name - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:publishedBy', # i3d:publishedBy - $service->authority - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:authoritative', # i3c:authoritative - $service->authoritative - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:description', # i3c:description - $service->description - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:endpoint', # i3c:endpoint - $service->URL - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:contributor', # dc:contributor - $service->contactEmail - ); - - $mdata.= rdfResource( - $lsid->as_string, - 'i3csp:performsTask', # i3csp:performsTask - 'urn:lsid:biomoby.org:servicetype:'.($service->type) - ); - - - my $inputs = $service->input; - my @inputs = @{$inputs}; + my $storage = new RDF::Core::Storage::Memory; + my $model = new RDF::Core::Model (Storage => $storage); - my $outputs = $service->output; - my @outputs = @{$outputs}; - - $mdata .= rdfBnode( - $lsid->as_string, - 'i3csp:primaryInput', # primaryInput bnode - 'primaryInput' - ); - my $in=0; - foreach (@inputs){ - ++$in; - $mdata .= rdfBnodeBnode( - 'primaryInput', - 'i3csp:primaryParameter', # primaryParameter bnode - "primaryParameter$in" - ); - $mdata .= rdfBnodeLiteral( - "primaryParameter$in", - 'i3csp:parameterName', - $_->articleName - ); - if ($_->isSimple){ - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterType', - 'i3csp:mobySimpleType' - ); - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($_->objectType) - ); - } else { - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterType', - 'i3csp:mobyCollectionType' - ); - my $simps = $_->Simples; - foreach my $simp(@{$simps}){ - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($simp->objectType) - ); - } - } - } - - $mdata .= rdfBnode( - $lsid->as_string, - 'i3csp:primaryOutput', # primaryInput bnode - 'primaryOutput' - ); - my $out= $in; # switch for readability - foreach (@outputs){ - ++$out; - $mdata .= rdfBnodeBnode( - 'primaryOutput', - 'i3csp:primaryParameter', # primaryParameter bnode - "primaryParameter$out" - ); - $mdata .= rdfBnodeLiteral( - "primaryParameter$out", - 'i3csp:parameterName', - $_->articleName - ); - if ($_->isSimple){ - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterType', - 'i3csp:mobySimpleType' - ); - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($_->objectType) - ); - } else { - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterType', - 'i3csp:mobyCollectionType' - ); - my $simps = $_->Simples; - foreach my $simp(@{$simps}){ - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($simp->objectType) - ); - } - } + foreach my $service(@{$si}){ + my $ServInstRDF = MOBY::RDF::ServiceInstanceRDF->new( + model => $model, + service_instance => $service, + ); } - - # +++++++++++ now we need the secondaries ++++++++ - $mdata.= $RDF_SUFFIX; - $RDF_SUFFIX?1:1; - - unless ($mdata) { - _die ('NO_METADATA_AVAILABLE'); - } - return $mdata; + print header(-type => 'application/rdf+xml', -expires => 'now'); + _serialize($model); + exit 1; } + +1; From mwilkinson at pub.open-bio.org Thu Jul 29 12:11:41 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 12:11:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407291611.i6TGBfMA019343@pub.open-bio.org> mwilkinson Thu Jul 29 12:11:40 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv19324/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: adding support for secondaries into the RDF generating routines moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 00:22:21 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 16:11:40 1.7 @@ -15,11 +15,13 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; -{ +{ # these need to be class variables, since this module is loaded multiple times, but the newResouce counter has to increment nevertheless. + my $inputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $outputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $simplefactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $collectionfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $secondaryfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:secondary', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); sub nextinput { return $inputfactory->newResource @@ -33,9 +35,14 @@ sub nextcollection { return $collectionfactory->newResource } + sub nextsecondary { + return $secondaryfactory->newResource + } } + + sub type { my ($self, @args) = @_; $args[0] && ($self->{type} = $args[0]); @@ -116,7 +123,7 @@ my $li = 0; foreach my $IN(@articles){ ++$li; - my $LI = $Thingy->new(RDF_NS, "_$li"); + my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc my $input = &nextsimple; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); $model->addStmt($statement); @@ -125,18 +132,18 @@ if ($IN->isSimple){ &_addSimple($model, $input, $IN); - } else { # COLLECTION + } elsif ($IN->isCollection) { # COLLECTION - is just a bag of simples my $type = $input->new(RDF_NS,'type'); my $statement = new RDF::Core::Statement($input, $type, $Bag); $model->addStmt($statement); # - _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; + _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; # the bag has an articlename my $simps = $IN->Simples; my $lli=0; foreach my $simp(@{$simps}){ ++$lli; - my $LI = $input->new(RDF_NS, "_$lli"); + my $LI = $input->new(RDF_NS, "_$lli"); # nodes - need to be numbered :_1, :_2, etc; these connect to the individual simples my $collection_member = &nextcollection; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); @@ -144,6 +151,10 @@ &_addSimple($model, $collection_member, $simp); } + } elsif ($IN->isSecondary) { + &_addSecondary($model, $input, $IN); + } else { + print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; } } } @@ -166,6 +177,27 @@ } +#| secondary_input_id | int(10) unsigned | | PRI | NULL | auto_increment | +#| default_value | text | YES | | NULL | | +#| maximum_value | decimal(10,0) | YES | | NULL | | +#| minimum_value | decimal(10,0) | YES | | NULL | | +#| enum_value | text | YES | | NULL | | +#| datatype | enum('String','Integer','DateTime','Float') | YES | | NULL | | +#| article_name | varchar(255) | YES | | NULL | | +#| service_instance_id | int(10) unsigned | | | 0 | | +sub _addSecondary { + my ($model, $article, $ART) = @_; # (RDF::COre::Model, $RDF::Core::Resource, $MOBY::Client::SimpleArticle) + _addClassLiteral($model, MP, $article, 'article_name', $ART->articleName) if $ART->articleName; + _addClassLiteral($model, MP, $article, 'default_value', $ART->default) if $ART->default; + _addClassLiteral($model, MP, $article, 'datatype', $ART->datatype) if $ART->datatype; + _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; + _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; + my @enums = $ART->enum; + foreach (@enums){ + _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; + } + +} sub _addResource { my ($model, $ns, $predicate, $subject, $ons, $object) = @_; From mwilkinson at pub.open-bio.org Thu Jul 29 13:49:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 13:49:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407291749.i6THnIfq019710@pub.open-bio.org> mwilkinson Thu Jul 29 13:49:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv19691/MOBY/lsid/authority Modified Files: metadata.pl Log Message: LSID's are no longer case sensitive in the new LS::* stack from IBM moby-live/Perl/MOBY/lsid/authority metadata.pl,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl 2004/01/15 20:59:38 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl 2004/07/29 17:49:18 1.5 @@ -28,13 +28,13 @@ use MOBY::lsid::authority::ServiceInstanceResolver qw(:all); my %known_types = ( # switch on/off various LSID-namespace resolvers. - 'namespacetype' => 1, - 'objectclass' => 1, - 'servicetype' => 1, - 'servicerelation' => 1, - 'objectrelation' => 1, - 'serviceinstance' => 1, - 'rdfpredicate' => 1, + 'NamespaceType' => 1, + 'ObjectClass' => 1, + 'ServiceType' => 1, + 'ServiceRelation' => 1, + 'ObjectRelation' => 1, + 'ServiceInstance' => 1, + 'MOBYSPredicate' => 1, ); MetaData(); @@ -68,13 +68,13 @@ _die("UNKNOWN_LSID"); } - return resolve_namespacetype($namespacedb,$lsid) if $1 eq "namespacetype"; - return resolve_classtype($objectdb,$lsid) if $1 eq "objectclass"; - return resolve_servicetype($servicedb,$lsid) if $1 eq "servicetype"; - return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "objectrelation"; - return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "servicerelation"; - return resolve_mobyPredicate($lsid) if $1 eq "rdfpredicate"; - return resolve_ServiceInstance($lsid) if $1 eq "serviceinstance"; + return resolve_namespacetype($namespacedb,$lsid) if $1 =~ /namespacetype/i; + return resolve_classtype($objectdb,$lsid) if $1 =~ /objectclass/i; + return resolve_servicetype($servicedb,$lsid) if $1 =~ /servicetype/i; + return resolve_relationshiptype($relationshipdb,$lsid) if $1 =~ /objectrelation/i; + return resolve_relationshiptype($relationshipdb,$lsid) if $1 =~ /servicerelation/i; + return resolve_mobyPredicate($lsid) if $1 =~ /rdfpredicate/i; + return resolve_ServiceInstance($lsid) if $1 =~ /serviceinstance/i; } From mwilkinson at pub.open-bio.org Thu Jul 29 17:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 17:53:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrsHH020286@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY/Client Modified Files: Central.pm Registration.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY/Client Central.pm,1.76,1.77 Registration.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.76 retrieving revision 1.77 diff -u -r1.76 -r1.77 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/06/16 01:15:30 1.76 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/29 21:53:54 1.77 @@ -1654,10 +1654,12 @@ my $id = &_nodeTextContent($Object, 'id'); my $success = &_nodeTextContent($Object, 'success'); my $message = &_nodeTextContent($Object, 'message'); + my $RDF = &_nodeTextContent($Object, 'RDF'); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, registration_id => $id, + RDF => $RDF, id => $id); return $reg; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2003/06/06 00:45:47 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/07/29 21:53:54 1.5 @@ -81,6 +81,7 @@ success => [0, 'read/write'], message => ["OK", 'read/write'], registration_id => [undef, 'read/write'], + RDF => [undef, 'read/write'], ); #_____________________________________________________________ From mwilkinson at pub.open-bio.org Thu Jul 29 17:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 17:53:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrsB1020305@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 00:22:21 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 21:53:54 1.6 @@ -15,6 +15,33 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +sub xmlNamespaces { + return { + RDF_NS() => 'rdf', + RDFS_NS() => 'rdfs', + OBJ() => 'mobyObject', + NS() => 'mobyNamespace', + SRV() => 'mobyService', + MP() => 'mobyPred', + SI() => 'serviceInstances', + DC() => 'dc', + } +} + + +sub serialize { + my ($model) = @_; + my $xml = ''; + + my $serializer = new RDF::Core::Model::Serializer( + Model=>$model, + Output=>\$xml, + getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! + ); + $serializer->serialize; + return $xml; +} + sub model { my ($self, @args) = @_; $args[0] && ($self->{model} = $args[0]); From mwilkinson at pub.open-bio.org Thu Jul 29 17:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 17:53:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrspw020263@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY Modified Files: Central.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY Central.pm,1.133,1.134 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.133 retrieving revision 1.134 diff -u -r1.133 -r1.134 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/12 00:39:37 1.133 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 21:53:53 1.134 @@ -22,6 +22,14 @@ use MOBY::secondary_input; use MOBY::central_db_connection; use MOBY::Config; +use MOBY::RDF::ServiceInstanceRDF; +use RDF::Core; +use RDF::Core::Model; +use RDF::Core::Literal; +use RDF::Core::Statement; +use RDF::Core::Model::Serializer; +use RDF::Core::Storage::Memory; +use RDF::Core::Constants qw(:xml :rdf :rdfs); my $debug = 0; @@ -153,11 +161,15 @@ my $id = $details->{id}; my $success = $details->{success}; my $message = $details->{message}; + my $RDF = ""; + $RDF = $details->{RDF}; + return " $id $success + "; } @@ -1149,7 +1161,36 @@ return &_error("Registration Failed During SECONDARY Article Registration: $msg","") unless ($success==1); } - return &_success("Registration successful", $SVC->service_instance_id); + # we're going to do a findService here to find the service that we just created + # and use the resulting XML to create a MOBY::Client::ServiceInstance object + # that we can then use to retrieve the RDF for that service signature. + # this is roundabout, I agree, but it is the most re-usable way to go at + # the moment. + + my ($si, $reg) = &findService(qw{ + + + $AuthURI; + $serviceName; + + "}); + unless ($si){ + $SVC->DELETE_THYSELF; + return &_error("Registration Failed - newly registered service could not be discovered",""); + } + my $service = shift @{$si}; + unless ($service){ + $SVC->DELETE_THYSELF; + return &_error("Registration Failed - newly registered service could not be discovered",""); + } + + my $services = MOBY::Client::Central::_parseServices('', '', $service); + my $service_instance = shift @{$services}; + my $storage = new RDF::Core::Storage::Memory; + my $model = new RDF::Core::Model (Storage => $storage); + my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(model => $model, service_instance => $service_instance); + my $RDF_XML = $RDF_MODEL->serialize; + return &_success("Registration successful", $SVC->service_instance_id, $RDF_XML); } sub _registerArticles { @@ -2977,11 +3018,12 @@ } sub _success { - my ($message, $id) = @_; + my ($message, $id, $RDF) = @_; my $reg = &Registration({ success => 1, message => "$message", id => "$id", + RDF => $RDF, }); return $reg; } From gss at pub.open-bio.org Thu Jul 29 19:30:12 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:30:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292330.i6TNUCwS020618@pub.open-bio.org> gss Thu Jul 29 19:30:12 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv20593/src/org/smoby/parser/test Modified Files: Test.java Log Message: Removed unused import statement moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java 2004/06/16 23:29:32 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java 2004/07/29 23:30:12 1.3 @@ -4,7 +4,6 @@ import java.util.*; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.parser.*; import com.hp.hpl.jena.rdf.model.*; From gss at pub.open-bio.org Thu Jul 29 19:31:44 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:31:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292331.i6TNViBj020675@pub.open-bio.org> gss Thu Jul 29 19:31:44 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv20626/src/org/smoby/graph/impl Removed Files: MOBYProviderSetImpl.java MOBYProviderImpl.java MOBYResizableCollectionImpl.java MOBYUnorderedCollectionImpl.java MOBYDateConstraintImpl.java MOBYPropertyValueStatementImpl.java MOBYDocumentImpl.java MOBYLiteralImpl.java MOBYOntologyImpl.java MOBYEnumerationImpl.java MOBYSubjectImpl.java MOBYGraphNodeImpl.java MOBYObjectFactory.java MOBYFixedCollectionImpl.java MOBYIntegerConstraintImpl.java MOBYObjectImpl.java MOBYPropertyValueConstraintImpl.java MOBYPropertyValueImpl.java MOBYMappingElementImpl.java MOBYGraphImpl.java MOBYNonPositiveIntegerConstraintImpl.java MOBYNumericConstraintImpl.java MOBYNonNegativeIntegerConstraintImpl.java MOBYOrderedCollectionImpl.java MOBYResourceImpl.java MOBYDescriptorImpl.java MOBYCollectionImpl.java MOBYSingleElementImpl.java Log Message: No longer separate graph interfaces from classes moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderSetImpl.java,1.1,NONE MOBYProviderImpl.java,1.2,NONE MOBYResizableCollectionImpl.java,1.2,NONE MOBYUnorderedCollectionImpl.java,1.2,NONE MOBYDateConstraintImpl.java,1.1,NONE MOBYPropertyValueStatementImpl.java,1.1,NONE MOBYDocumentImpl.java,1.2,NONE MOBYLiteralImpl.java,1.1,NONE MOBYOntologyImpl.java,1.2,NONE MOBYEnumerationImpl.java,1.2,NONE MOBYSubjectImpl.java,1.2,NONE MOBYGraphNodeImpl.java,1.2,NONE MOBYObjectFactory.java,1.3,NONE MOBYFixedCollectionImpl.java,1.2,NONE MOBYIntegerConstraintImpl.java,1.1,NONE MOBYObjectImpl.java,1.2,NONE MOBYPropertyValueConstraintImpl.java,1.1,NONE MOBYPropertyValueImpl.java,1.1,NONE MOBYMappingElementImpl.java,1.2,NONE MOBYGraphImpl.java,1.2,NONE MOBYNonPositiveIntegerConstraintImpl.java,1.1,NONE MOBYNumericConstraintImpl.java,1.1,NONE MOBYNonNegativeIntegerConstraintImpl.java,1.1,NONE MOBYOrderedCollectionImpl.java,1.2,NONE MOBYResourceImpl.java,1.1,NONE MOBYDescriptorI! mpl.java,1.2,NONE MOBYCollectionImpl.java,1.2,NONE MOBYSingleElementImpl.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYProviderSetImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYProviderImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYResizableCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYUnorderedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDateConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueStatementImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDocumentImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYLiteralImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYOntologyImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYEnumerationImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYSubjectImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYGraphNodeImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYObjectFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYFixedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYObjectImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYMappingElementImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYGraphImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNonPositiveIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNumericConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNonNegativeIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYOrderedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYResourceImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDescriptorImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYSingleElementImpl.java,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 19:33:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:33:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292333.i6TNXxG9020829@pub.open-bio.org> gss Thu Jul 29 19:33:59 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv20716/src/org/smoby/graph Modified Files: MOBYDocument.java MOBYLiteral.java MOBYResource.java MOBYFixedCollection.java MOBYResizableCollection.java MOBYSingleElement.java MOBYPropertyValueConstraint.java MOBYPropertyValueStatement.java MOBYEnumeration.java MOBYProvider.java MOBYPropertyValue.java MOBYOntology.java MOBYProviderSet.java MOBYMappingElement.java MOBYDescriptor.java MOBYOrderedCollection.java MOBYCollection.java MOBYUnorderedCollection.java MOBYGraph.java MOBYGraphNode.java MOBYObject.java MOBYSubject.java MOBYPropertyValueException.java Added Files: MOBYIntegerConstraint.java MOBYDateConstraint.java MOBYNonNegativeIntegerConstraint.java MOBYNumericConstraint.java MOBYNonPositiveIntegerConstraint.java Log Message: No longer separate graph interfaces from classes moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYIntegerConstraint.java,NONE,1.1 MOBYDateConstraint.java,NONE,1.1 MOBYNonNegativeIntegerConstraint.java,NONE,1.1 MOBYNumericConstraint.java,NONE,1.1 MOBYNonPositiveIntegerConstraint.java,NONE,1.1 MOBYDocument.java,1.1,1.2 MOBYLiteral.java,1.1,1.2 MOBYResource.java,1.1,1.2 MOBYFixedCollection.java,1.1,1.2 MOBYResizableCollection.java,1.1,1.2 MOBYSingleElement.java,1.1,1.2 MOBYPropertyValueConstraint.java,1.1,1.2 MOBYPropertyValueStatement.java,1.1,1.2 MOBYEnumeration.java,1.1,1.2 MOBYProvider.java,1.1,1.2 MOBYPropertyValue.java,1.1,1.2 MOBYOntology.java,1.1,1.2 MOBYProviderSet.java,1.1,1.2 MOBYMappingElement.java,1.1,1.2 MOBYDescriptor.java,1.2,1.3 MOBYOrderedCollection.java,1.1,1.2 MOBYCollection.java,1.1,1.2 MOBYUnorderedCollection.java,1.1,1.2 MOBYGraph.java,1.1,1.2 MOBYGraphNode.java,1.1,1.2 MOBYObject.java,1.1,1.2 MOBYSubject.java,1.1,1.2 MOBYPropertyValueException.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,15 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents a document to be incorporated into + * This class represents a document to be incorporated into * the S-MOBY metadata repository. */ -public interface MOBYDocument extends MOBYDescriptor +public abstract class MOBYDocument extends MOBYDescriptor { + public MOBYDocument(Resource resource, Model underlying) + { + super(resource, underlying); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java 2004/07/29 23:33:59 1.2 @@ -1,7 +1,24 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.Literal; -public interface MOBYLiteral extends MOBYPropertyValue +public class MOBYLiteral extends MOBYPropertyValue { - public String getStringValue(); -} \ No newline at end of file + private String stringValue; + + public MOBYLiteral(String stringValue) { + this.stringValue = stringValue; + } + + public String getStringValue() { + return stringValue; + } + + public boolean isLiteral() { + return true; + } + + public boolean isResource() { + return false; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,29 @@ package org.smoby.graph; +import org.smoby.graph.*; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYResource extends MOBYPropertyValue +public class MOBYResource extends MOBYPropertyValue { - public String getResourceURI(); - public boolean isBlank(); + private Resource resourceValue; + + public MOBYResource(Resource resourceValue) { + this.resourceValue = resourceValue; + } + + public String getResourceURI() { + return resourceValue.getURI(); + } + + public boolean isLiteral() { + return false; + } + + public boolean isResource() { + return true; + } + + public boolean isBlank() { + return resourceValue.isAnon(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,20 @@ package org.smoby.graph; +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface representing unordered, fixed sized collection + * A class representing unordered, fixed sized collection * of objects. */ -public interface MOBYFixedCollection extends MOBYCollection +public class MOBYFixedCollection extends MOBYCollection { -} \ No newline at end of file + + public MOBYFixedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isResizable() { return false; } + public boolean isFixedSized() { return true; } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java 2004/07/29 23:33:59 1.2 @@ -1,14 +1,29 @@ package org.smoby.graph; +import java.util.*; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface representing collections that can be resized (i.e. + * A class representing collections that can be resized (i.e. * elements added to or removed from); such collections can be * either ordered or unordered. */ -public interface MOBYResizableCollection extends MOBYCollection +public abstract class MOBYResizableCollection extends MOBYCollection { + public MOBYResizableCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + /** * Return whether or not this collection is ordered. */ - public boolean isOrdered(); -} \ No newline at end of file + public abstract boolean isOrdered(); + + public boolean isResizable() { return true; } + public boolean isFixedSized() { return false; } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,23 @@ package org.smoby.graph; +import java.net.URI; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface to represent singular objects, i.e. those that are + * A class to represent singular objects, i.e. those that are * not collections. */ -public interface MOBYSingleElement extends MOBYGraphNode +public abstract class MOBYSingleElement extends MOBYGraphNode { -} + public MOBYSingleElement(Resource resource, Model underlying) + { + super(resource, underlying); + } + + public boolean isSingular() { return true; } + public boolean isCollection() { return false; } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,9 @@ package org.smoby.graph; -public interface MOBYPropertyValueConstraint +public abstract class MOBYPropertyValueConstraint { - public void validatePropertyValue(MOBYPropertyValueStatement stmt, - MOBYPropertyValue newValue) + public abstract void validatePropertyValue( + MOBYPropertyValueStatement stmt, + MOBYPropertyValue newValue) throws MOBYPropertyValueException; } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java 2004/07/29 23:33:59 1.2 @@ -1,28 +1,76 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYPropertyValueStatement +public class MOBYPropertyValueStatement extends MOBYDescriptor { + private Statement jenaStatement; + private MOBYPropertyValue currentValue; + private MOBYPropertyValueConstraint constraint; + + public MOBYPropertyValueStatement(Statement jenaStatement, + Model underlying) { + super(null, underlying); + this.jenaStatement = jenaStatement; + if (jenaStatement.getObject().canAs(Resource.class)) { + Resource value = (Resource) jenaStatement.getObject(); + currentValue = new MOBYResource(value); + } else { + Literal value = (Literal) jenaStatement.getObject(); + currentValue = new MOBYLiteral(value.getString()); + } + } + /** * Return the name of this property */ - public String getPropertyName(); + public String getPropertyName() { + return jenaStatement.getPredicate().getURI(); + } + public String toString() { + return jenaStatement.toString(); + } + /** * Return the value currently associated with this property */ - public MOBYPropertyValue getValue(); - + public MOBYPropertyValue getValue() { + return currentValue; + } + /** * Set the property value. This is just a placeholder; values of * different property types will be set to different types of * values. */ public void setPropertyValue(MOBYPropertyValue newValue) - throws MOBYPropertyValueException; - + throws MOBYPropertyValueException + { + if (constraint != null) { + constraint.validatePropertyValue(this, newValue); + } + + if (newValue.isLiteral()) { + MOBYLiteral literal = (MOBYLiteral) newValue; + jenaStatement.changeObject(literal.getStringValue()); + } else { + MOBYResource resource = (MOBYResource) newValue; + if (resource.isBlank()) { + jenaStatement.changeObject( + jenaStatement.getModel().createResource()); + } else { + jenaStatement.changeObject( + jenaStatement.getModel().createResource( + resource.getResourceURI())); + } + } + } + /** * Set the given constraint for this property value statement */ - public void setConstraint(MOBYPropertyValueConstraint constraint); -} \ No newline at end of file + public void setConstraint(MOBYPropertyValueConstraint constraint) { + this.constraint = constraint; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java 2004/07/29 23:33:59 1.2 @@ -1,10 +1,19 @@ package org.smoby.graph; +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface representing a resizable collection of objects, in + * A class representing a resizable collection of objects, in * which the order of the elements is not defined; the intention is * for the elements to represent possible choices for a value. */ -public interface MOBYEnumeration extends MOBYUnorderedCollection +public class MOBYEnumeration extends MOBYUnorderedCollection { -} + public MOBYEnumeration(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isEnumeration() { return true; } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java 2004/07/29 23:33:59 1.2 @@ -1,38 +1,84 @@ package org.smoby.graph; import java.io.*; +import com.hp.hpl.jena.rdf.model.*; /** - * The Provider interface represents a resource that provides a + * The Provider class represents a resource that provides a * service in MOBY. */ -public interface MOBYProvider extends MOBYDocument +public class MOBYProvider extends MOBYDocument { + private String name; + private String oneLineDescription; + private String moreInfoURI; + private MOBYUnorderedCollection operatesOn; + + public MOBYProvider(Resource resource, String name, String oneLineDescription, + String moreInfoURI, MOBYUnorderedCollection operatesOn, + Model underlying) + { + super(resource, underlying); + this.name = name; + this.oneLineDescription = oneLineDescription; + this.moreInfoURI = moreInfoURI; + this.operatesOn = operatesOn; + } + /** * Return a descriptive name for the provider. */ - public String getName(); - + public String getName() + { + return name; + } + /** * Return a short (one line) description for the provider. */ - public String getOneLineDescription(); - + public String getOneLineDescription() + { + return oneLineDescription; + } + /** * Return a URI that can be accessed to obtain more information * about the provider. */ - public String getMoreInfoURI(); + public String getMoreInfoURI() + { + return moreInfoURI; + } /** * Return a collection of graph nodes that this provider operates on. * Each graph node represents either a Graph or GraphCollection. */ - public MOBYUnorderedCollection getOperatesOn(); + public MOBYUnorderedCollection getOperatesOn() + { + return operatesOn; + } + public String toString() + { + StringBuffer sb = new StringBuffer(); + sb.append("Provider [name=\""); + sb.append(name); + sb.append("\", oneLineDescription=\""); + sb.append(oneLineDescription); + sb.append("\", moreInfoURI="); + sb.append(moreInfoURI); + sb.append("\"]"); + + return sb.toString(); + } + /** - * Provider implementations should be capable of serializing themselves + * Providers should be capable of serializing themselves * to an output stream */ - public void serialize(OutputStream out); -} \ No newline at end of file + public void serialize(OutputStream out) + { + underlying.write(out); + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java 2004/07/29 23:33:59 1.2 @@ -1,18 +1,22 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.Model; + /** - * A superinterface for things that can appear as the subject + * A superclass for things that can appear as the subject * or object of a statement. */ -public interface MOBYPropertyValue +public abstract class MOBYPropertyValue { /** - * Return whether or not this property value represents a literal + * Return whether or not this property value represents + * a literal value */ - public boolean isLiteral(); - + public abstract boolean isLiteral(); + /** - * Return whether or not this property value represents a resource + * Return whether or not this property value represents + * a resource */ - public boolean isResource(); + public abstract boolean isResource(); } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,14 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents a collection of RDF statements to be + * This class represents a collection of RDF statements to be * incorporated into the S-MOBY metadata repository. */ -public interface MOBYOntology extends MOBYDocument +public class MOBYOntology extends MOBYDocument { -} + public MOBYOntology(Resource resource, Model underlying) { + super(resource, underlying); + } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java 2004/06/18 21:37:52 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java 2004/07/29 23:33:59 1.2 @@ -1,25 +1,56 @@ package org.smoby.graph; import java.io.*; +import java.util.*; +import org.smoby.tools.*; +import com.hp.hpl.jena.rdf.model.*; /** - * An interface to represent a set of providers + * An class to represent a set of providers */ -public interface MOBYProviderSet extends MOBYDocument +public class MOBYProviderSet extends MOBYDocument { + private List providers = new ArrayList(); + + public MOBYProviderSet() + { + super(null, null); + } + /** - * Add a provider to the set + * Return the size of the set */ - public void addProvider(MOBYProvider provider); - + public int size() + { + return providers.size(); + } + /** - * Return the size of the set + * Add a provider to the set */ - public int size(); - + public void addProvider(MOBYProvider provider) + { + providers.add(provider); + } + /** * Provider sets should be capable of serializing themselves * to an output stream */ - public void serialize(OutputStream out); + public void serialize(OutputStream out) + { + Model merged = ModelFactory.createDefaultModel(); + + for (Iterator it = providers.iterator(); it.hasNext();) + { + MOBYProvider provider = (MOBYProvider) it.next(); + Model underlying = provider.getUnderlying(); + merged.add(underlying); + merged.setNsPrefixes(underlying.getNsPrefixMap()); + } + + Util.removeUnusedNsPrefixes(merged); + + merged.write(out); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java 2004/07/29 23:33:59 1.2 @@ -1,17 +1,36 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYMappingElement extends MOBYSingleElement + +public class MOBYMappingElement extends MOBYSingleElement { + private MOBYFixedCollection statements; + private MOBYCollection nestedElements; + + public MOBYMappingElement(Resource resource, MOBYFixedCollection statements, + MOBYCollection nestedElements, Model underlying) + { + super(resource, underlying); + this.statements = statements; + this.nestedElements = nestedElements; + } + /** * Return the collection of property-setting statements associated - * with this subject. + * with this mapping element. */ - public MOBYFixedCollection getPropertyValueStatements(); - + public MOBYFixedCollection getPropertyValueStatements() + { + return statements; + } + /** - * Return the collection of mappings that are nested within this subject - * through its role as a data structure. + * Return the collection of mappings that are nested within this + * mapping element through its role as a data structure. */ - public MOBYCollection getNestedElements(); + public MOBYCollection getNestedElements() { + return nestedElements; + } + } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/19 18:21:36 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/29 23:33:59 1.3 @@ -1,17 +1,43 @@ package org.smoby.graph; -import java.net.URI; - -import com.hp.hpl.jena.rdf.model.Resource; +import com.hp.hpl.jena.rdf.model.*; /** - * The Resource interface represents things that are available + * The MOBYDescriptor class represents things that are available * at a URI. */ -public interface MOBYDescriptor +public abstract class MOBYDescriptor { + protected Model underlying; + protected Resource resource; + + public MOBYDescriptor(Resource resource, Model underlying) + { + this.resource = resource; + this.underlying = underlying; + } + + /** + * Return the resource associated with this descriptor. + */ + public Resource getResource() + { + return resource; + } + + /** + * Return the underlying Jena model + */ + public Model getUnderlying() + { + return underlying; + } + /** - * Return the URI represented by this node. + * Return the URI of the underlying resource, if any. */ - public Resource getResource(); -} + public String getURI() + { + return (resource == null) ? null : resource.getURI(); + } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,13 +1,22 @@ package org.smoby.graph; -/** - * An interface representing resizable collection of objects, in - * which the order of the elements is defined. - */ -public interface MOBYOrderedCollection extends MOBYResizableCollection +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + +public class MOBYOrderedCollection extends MOBYResizableCollection { + public MOBYOrderedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isOrdered() { return true; } + /** * Return the object at a given zero-based index. */ - public Object get(int index); + public Object get(int index) + { + return elements.get(index); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java 2004/07/29 23:33:59 1.2 @@ -1,30 +1,50 @@ package org.smoby.graph; -import java.util.Iterator; +import com.hp.hpl.jena.rdf.model.*; +import java.util.*; /** - * A common interface for collections, both fixed sized and resizeable, of - * elements in MOBY graphs. + * A common abstract class for collections, both fixed sized and resizeable, + * of elements in MOBY graphs. */ -public interface MOBYCollection extends MOBYGraphNode +public abstract class MOBYCollection extends MOBYGraphNode { + protected List elements = new ArrayList(); + + public MOBYCollection(Resource resource, List elements, Model underlying) + { + super(resource, underlying); + for (Iterator it = elements.iterator(); it.hasNext();) { + this.elements.add(it.next()); + } + } + /** - * Return whether or not the collection is fixed in size + * Return the size of the collection. */ - public boolean isFixedSized(); - + public int size() + { + return elements.size(); + } + /** - * Return whether or not the collection is resizable + * Return an iterator for traversing the elements */ - public boolean isResizable(); + public Iterator iterator() + { + return elements.iterator(); + } /** - * Return an iterator for traversing the elements + * Return whether or not the collection is fixed in size */ - public Iterator iterator(); + public abstract boolean isFixedSized(); /** - * Return the size of the collection. + * Return whether or not the collection is resizable */ - public int size(); + public abstract boolean isResizable(); + + public boolean isSingular() { return false; } + public boolean isCollection() { return true; } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,14 +1,28 @@ package org.smoby.graph; +import java.util.*; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface representing resizable collection of objects, in + * A class representing resizable collection of objects, in * which the order of the elements is not defined. */ -public interface MOBYUnorderedCollection extends MOBYResizableCollection +public class MOBYUnorderedCollection extends MOBYResizableCollection { + public MOBYUnorderedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isOrdered() { return false; } + /** * Return whether or not the elements of this collection represent * choices (i.e. elements of an enumeration of possible values). */ - public boolean isEnumeration(); + public boolean isEnumeration() { return false; } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java 2004/07/29 23:33:59 1.2 @@ -1,13 +1,26 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents singular (i.e. not collection) subgraphs + * This class represents singular (i.e. not collection) subgraphs * that have a single mapping. */ -public interface MOBYGraph extends MOBYSingleElement +public class MOBYGraph extends MOBYSingleElement { + private MOBYGraphNode hasMapping; + + public MOBYGraph(Resource resource, MOBYGraphNode hasMapping, Model underlying) + { + super(resource, underlying); + this.hasMapping = hasMapping; + } + /** * Return the object of this graph's hasMapping property. */ - public MOBYGraphNode gethasMapping(); + public MOBYGraphNode getHasMapping() + { + return hasMapping; + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java 2004/07/29 23:33:59 1.2 @@ -1,23 +1,33 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface for nodes in an RDF graph; these nodes are either + * An abstract class for nodes in an RDF graph; these nodes are either * collections or singular elements. */ -public interface MOBYGraphNode extends MOBYDescriptor +public abstract class MOBYGraphNode extends MOBYDescriptor { + public MOBYGraphNode(Resource resource, Model underlying) + { + super(resource, underlying); + } + /** * Return whether or not this node represents a blank node */ - public boolean isBlank(); + public boolean isBlank() + { + return (resource == null) || (resource.getURI() == null); + } /** * Return whether or not this object is a collection. */ - public boolean isCollection(); + public abstract boolean isCollection(); /** * Return whether or not this object is a singular element. */ - public boolean isSingular(); + public abstract boolean isSingular(); } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,15 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** * An object that represents the object of a mapping. */ -public interface MOBYObject extends MOBYMappingElement +public class MOBYObject extends MOBYMappingElement { -} \ No newline at end of file + public MOBYObject(Resource resource, MOBYFixedCollection statements, + MOBYCollection nestedElements, Model underlying) + { + super(resource, statements, nestedElements, underlying); + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java 2004/07/29 23:33:59 1.2 @@ -1,6 +1,9 @@ package org.smoby.graph; -import java.net.URI; +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; /** * An object that represents the subject of one or more mappings. In @@ -16,11 +19,27 @@ * of which can itself be either a moby:Subject, an RDF data structure, * or both. This collection of elements is returned by getNestedMappings(). */ -public interface MOBYSubject extends MOBYMappingElement +public class MOBYSubject extends MOBYMappingElement { + /** + * The collection of direct mappings, i.e. moby:mapsTo statements + * whose subject is this. + */ + private MOBYUnorderedCollection directMappings; + + public MOBYSubject(Resource resource, MOBYFixedCollection statements, + MOBYUnorderedCollection directMappings, + MOBYCollection nestedMappings, Model underlying) + { + super(resource, statements, nestedMappings, underlying); + this.directMappings = directMappings; + } + /** * Return a resizable, unordered collection of the MOBYNode instances, * which are objects of mapsTo statements, whose subjects are this. */ - public MOBYUnorderedCollection getDirectMappings(); -} \ No newline at end of file + public MOBYUnorderedCollection getDirectMappings() { + return directMappings; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java 2004/07/29 23:33:59 1.2 @@ -1,6 +1,5 @@ package org.smoby.graph; - public class MOBYPropertyValueException extends Exception { public MOBYPropertyValueException(String message) { From mwilkinson at pub.open-bio.org Thu Jul 29 19:34:06 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 19:34:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNY6mG020893@pub.open-bio.org> mwilkinson Thu Jul 29 19:34:06 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv20855/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: okay,now it works properly. A new parameter RDF is returned in the Registration XML. This holds the RDF signature of your service. moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 21:53:54 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 23:34:06 1.7 @@ -30,11 +30,11 @@ sub serialize { - my ($model) = @_; + my ($self) = @_; my $xml = ''; my $serializer = new RDF::Core::Model::Serializer( - Model=>$model, + Model=>$self->model, Output=>\$xml, getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! ); From mwilkinson at pub.open-bio.org Thu Jul 29 19:34:06 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 19:34:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNY6n7020874@pub.open-bio.org> mwilkinson Thu Jul 29 19:34:06 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv20855/MOBY Modified Files: Central.pm Log Message: okay,now it works properly. A new parameter RDF is returned in the Registration XML. This holds the RDF signature of your service. moby-live/Perl/MOBY Central.pm,1.134,1.135 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.134 retrieving revision 1.135 diff -u -r1.134 -r1.135 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 21:53:53 1.134 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 23:34:06 1.135 @@ -1167,24 +1167,19 @@ # this is roundabout, I agree, but it is the most re-usable way to go at # the moment. - my ($si, $reg) = &findService(qw{ + my ($si, $reg) = &findService('',' $AuthURI; $serviceName; - "}); + '); unless ($si){ $SVC->DELETE_THYSELF; return &_error("Registration Failed - newly registered service could not be discovered",""); } - my $service = shift @{$si}; - unless ($service){ - $SVC->DELETE_THYSELF; - return &_error("Registration Failed - newly registered service could not be discovered",""); - } - - my $services = MOBY::Client::Central::_parseServices('', '', $service); + use MOBY::Client::Central; + my $services = MOBY::Client::Central::_parseServices('', '', $si); my $service_instance = shift @{$services}; my $storage = new RDF::Core::Storage::Memory; my $model = new RDF::Core::Model (Storage => $storage); @@ -1670,7 +1665,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if (scalar @{$findme{keywords}}){ + if ($findme{keywords} && (scalar @{$findme{keywords}})){ ++$criterion_count; $debug && _LOG("Keywords added; criterion count is now $criterion_count\n"); my $searchstring; @@ -1694,7 +1689,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if (scalar @{$findme{inputObjects}}){ + if ($findme{inputObjects} && (scalar @{$findme{inputObjects}})){ ++$criterion_count; $debug && _LOG("inputObject added; criterion count is now $criterion_count\n"); my $obj = (shift @{$findme{inputObjects}}); @@ -1727,7 +1722,7 @@ ++$valid_service_ids{$_}; } } - if (scalar @{$findme{outputObjects}}){ + if ($findme{outputObjects} && (scalar @{$findme{outputObjects}})){ ++$criterion_count; $debug && _LOG("outputObject added; criterion count is now $criterion_count\n"); my $obj = (shift @{$findme{outputObjects}}); From gss at pub.open-bio.org Thu Jul 29 19:34:44 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:34:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNYi6a020925@pub.open-bio.org> gss Thu Jul 29 19:34:43 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools In directory pub.open-bio.org:/tmp/cvs-serv20901/src/org/smoby/graph/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools added to the repository moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 19:34:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:34:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNYks3020959@pub.open-bio.org> gss Thu Jul 29 19:34:45 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools In directory pub.open-bio.org:/tmp/cvs-serv20938/src/org/smoby/graph/tools Added Files: MOBYProviderTraversalException.java MOBYProviderXMLGenerator.java MOBYProviderVisitor.java MOBYProviderTraverser.java Log Message: Visitor pattern for MOBY graphs, with example moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools MOBYProviderTraversalException.java,NONE,1.1 MOBYProviderXMLGenerator.java,NONE,1.1 MOBYProviderVisitor.java,NONE,1.1 MOBYProviderTraverser.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 29 19:35:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:35:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292335.i6TNZ9Ta020991@pub.open-bio.org> gss Thu Jul 29 19:35:09 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv20966/src/org/smoby/parser Modified Files: Parser.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/19 18:21:36 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/29 23:35:09 1.7 @@ -4,7 +4,6 @@ import java.net.*; import java.util.*; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.parser.*; import org.smoby.tools.ModelRetriever; import org.smoby.tools.Util; @@ -179,7 +178,7 @@ // Create and return an unordered collection of the parsed providers // - return MOBYObjectFactory.newUnorderedCollection(null, providers, null); + return new MOBYUnorderedCollection(null, providers, null); } /** @@ -211,9 +210,9 @@ // Create and return a new Provider object using the provider URI, name, // oneLineDescription, aboutURI, and collection of operatesOn subgraphs // - return MOBYObjectFactory.newProvider( + return new MOBYProvider( provider, name, oneLiner, aboutURI, - MOBYObjectFactory.newUnorderedCollection(provider, operatesOn, model), + new MOBYUnorderedCollection(provider, operatesOn, model), model); } @@ -234,7 +233,7 @@ // hasMapping property that leads to its mapping subgraph. // Resource hasMapping = getResourcePropertyValue(res, MOBY.hasMapping); - return MOBYObjectFactory.newGraph(res, parseHasMapping(hasMapping), model); + return new MOBYGraph(res, parseHasMapping(hasMapping), model); } else { @@ -318,9 +317,9 @@ // Create and return a Subject to describe this hasMapping subgraph // - return MOBYObjectFactory.newSubject(res, - MOBYObjectFactory.newFixedCollection(res, statements, model), - MOBYObjectFactory.newUnorderedCollection(res, directMappings, model), + return new MOBYSubject(res, + new MOBYFixedCollection(res, statements, model), + new MOBYUnorderedCollection(res, directMappings, model), collectionFor(res, nestedMappings), model); } @@ -362,8 +361,8 @@ // Create and return a new MOBYObject // Model model = res.getModel(); - return MOBYObjectFactory.newObject(res, - MOBYObjectFactory.newFixedCollection(res, statements, model), + return new MOBYObject(res, + new MOBYFixedCollection(res, statements, model), collectionFor(res, nested), model); } @@ -395,7 +394,7 @@ if (isMobyProperty(p, model)) { MOBYPropertyValueStatement pvalStmt = - MOBYObjectFactory.newPropertyValueStatement(stmt, model); + new MOBYPropertyValueStatement(stmt, model); Statement s = p.getProperty(RDFS.range); @@ -403,15 +402,15 @@ { Resource range = (Resource) s.getObject(); if (range.equals(XSD.date)) { - pvalStmt.setConstraint(MOBYObjectFactory.newDateConstraint()); + pvalStmt.setConstraint(new MOBYDateConstraint()); } else if (range.equals(XSD.integer)) { - pvalStmt.setConstraint(MOBYObjectFactory.newIntegerConstraint()); + pvalStmt.setConstraint(new MOBYIntegerConstraint()); } else if (range.equals(XSD.nonNegativeInteger)) { pvalStmt.setConstraint( - MOBYObjectFactory.newNonNegativeIntegerConstraint()); + new MOBYNonNegativeIntegerConstraint()); } else if (range.equals(XSD.nonPositiveInteger)) { pvalStmt.setConstraint( - MOBYObjectFactory.newNonPositiveIntegerConstraint()); + new MOBYNonPositiveIntegerConstraint()); } } @@ -486,13 +485,13 @@ private MOBYCollection collectionFor(Resource res, List elements) { if (isList(res)) { - return MOBYObjectFactory.newFixedCollection(res, elements, res.getModel()); + return new MOBYFixedCollection(res, elements, res.getModel()); } else if (isBag(res)) { - return MOBYObjectFactory.newUnorderedCollection(res, elements, res.getModel()); + return new MOBYUnorderedCollection(res, elements, res.getModel()); } else if (isSeq(res)) { - return MOBYObjectFactory.newOrderedCollection(res, elements, res.getModel()); + return new MOBYOrderedCollection(res, elements, res.getModel()); } else if (isAlt(res)) { - return MOBYObjectFactory.newEnumeration(res, elements, res.getModel()); + return new MOBYEnumeration(res, elements, res.getModel()); } else { return null; } From gss at pub.open-bio.org Thu Jul 29 19:37:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:37:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292337.i6TNbxZw021051@pub.open-bio.org> gss Thu Jul 29 19:37:59 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21026/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools DiscoveryQuery.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/15 20:27:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/29 23:37:59 1.2 @@ -8,7 +8,6 @@ import org.smoby.ref.tools.db.*; import org.smoby.tools.Util; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.vocabulary.*; import com.hp.hpl.jena.db.*; @@ -111,7 +110,7 @@ Model dbModel = null; try { - Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying(); + Model queryModel = ((MOBYProvider) queryProvider).getUnderlying(); String queryString = buildQueryString(queryModel); StorageManager manager = new StorageManager(); dbModel = manager.openDBModel(); @@ -129,7 +128,7 @@ } results.close(); - MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet(); + MOBYProviderSet returnSet = new MOBYProviderSet(); for (Iterator it = matching.iterator(); it.hasNext();) { From gss at pub.open-bio.org Thu Jul 29 19:38:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:38:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292338.i6TNce9x021089@pub.open-bio.org> gss Thu Jul 29 19:38:40 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv21064/src/org/smoby/ref/servlets/example Modified Files: HelloWorldServlet.java Log Message: Remove use of MOBYObjectFactory moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/21 22:01:19 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/29 23:38:40 1.3 @@ -6,7 +6,6 @@ import javax.servlet.http.*; import org.smoby.graph.*; -import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.ref.servlets.*; import org.smoby.servlet.*; @@ -34,7 +33,7 @@ MOBYGraph graph = (MOBYGraph) provider.getOperatesOn().iterator().next(); - MOBYSubject subject = (MOBYSubject) graph.gethasMapping(); + MOBYSubject subject = (MOBYSubject) graph.getHasMapping(); MOBYObject object = (MOBYObject) subject.getDirectMappings().iterator().next(); @@ -43,7 +42,7 @@ object.getPropertyValueStatements().iterator().next(); stmt.setPropertyValue( - MOBYObjectFactory.newLiteralValue("Hello, world!")); + new MOBYLiteral("Hello, world!")); } // Silently ignore graphs without the required form From gss at pub.open-bio.org Thu Jul 29 19:38:53 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:38:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292338.i6TNcr5E021119@pub.open-bio.org> gss Thu Jul 29 19:38:53 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21094/src/org/smoby/ref/tools Modified Files: KeywordFinder.java Log Message: Remove use of MOBYObjectFactory moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools KeywordFinder.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java 2004/07/21 22:01:19 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java 2004/07/29 23:38:53 1.2 @@ -85,7 +85,7 @@ if (node instanceof MOBYGraph) { MOBYGraph graph = (MOBYGraph) node; - addSubjectKeywordsFor(graph.gethasMapping()); + addSubjectKeywordsFor(graph.getHasMapping()); } else if (node instanceof MOBYCollection) { From gss at pub.open-bio.org Thu Jul 29 19:39:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:39:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292339.i6TNdH12021149@pub.open-bio.org> gss Thu Jul 29 19:39:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv21124/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageManager.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/29 23:39:17 1.3 @@ -1,7 +1,6 @@ package org.smoby.ref.tools.db; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.ref.tools.*; import org.smoby.tools.Util; import org.smoby.vocabulary.*; @@ -60,7 +59,7 @@ public void registerProvider(MOBYProvider provider, Date lastModifiedDate) throws StorageException { - Model model = ((MOBYProviderImpl) provider).getUnderlying(); + Model model = ((MOBYProvider) provider).getUnderlying(); Model dbModel = null; String uriString = provider.getResource().getURI(); Resource uri = model.createResource(uriString); From gss at pub.open-bio.org Thu Jul 29 19:44:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNiaFR021283@pub.open-bio.org> gss Thu Jul 29 19:44:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc In directory pub.open-bio.org:/tmp/cvs-serv21259/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 19:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicbn021313@pub.open-bio.org> gss Thu Jul 29 19:44:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/15 20:30:18 1.11 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/29 23:44:37 1.12 @@ -6,7 +6,6 @@ import javax.servlet.http.*; import org.smoby.servlet.*; import org.smoby.graph.*; -import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.vocabulary.*; import com.acmepubs.vocabulary.*; @@ -54,7 +53,7 @@ // The subject of the graph should be a MOBYSubject // - MOBYSubject subject = (MOBYSubject) graph.gethasMapping(); + MOBYSubject subject = (MOBYSubject) graph.getHasMapping(); // That object should have a single subproperty of moby:Property, // namely geneSymbol; its value should be a literal @@ -77,8 +76,7 @@ // based on a base URI string and the geneSymbol that was passed // String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus="; - literal = MOBYObjectFactory.newLiteralValue( - baseURI + geneSymbol); + literal = new MOBYLiteral(baseURI + geneSymbol); stmt.setPropertyValue(literal); } } From gss at pub.open-bio.org Thu Jul 29 19:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNic60021333@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/server/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/06/18 21:42:34 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/29 23:44:38 1.7 @@ -111,7 +111,7 @@ Model dbModel = null; try { - Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying(); + Model queryModel = queryProvider.getUnderlying(); String queryString = buildQueryString(queryModel); StorageManager manager = new StorageManager(); dbModel = manager.openDBModel(); @@ -129,7 +129,7 @@ } results.close(); - MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet(); + MOBYProviderSet returnSet = new MOBYProviderSet(); for (Iterator it = matching.iterator(); it.hasNext();) { From gss at pub.open-bio.org Thu Jul 29 19:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicgw021373@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/06/18 21:42:34 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/29 23:44:38 1.6 @@ -58,7 +58,7 @@ public void registerProvider(MOBYProvider provider, Date lastModifiedDate) throws StorageException { - Model model = ((MOBYProviderImpl) provider).getUnderlying(); + Model model = provider.getUnderlying(); Model dbModel = null; String uriString = provider.getURI(); Resource uri = model.createResource(uriString); From gss at pub.open-bio.org Thu Jul 29 19:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicra021352@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients Modified Files: SimpleProviderEngagerPanel.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/15 20:20:37 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/29 23:44:38 1.3 @@ -120,7 +120,7 @@ } else { - String graphURI = provider.getURI(); + String graphURI = provider.getResource().getURI(); HTTPRequest request = HTTPRequest.newPostRequest(graphURI); request.addParameter("graph", graphString); HTTPResponse response = request.send(); From mwilkinson at pub.open-bio.org Thu Jul 29 20:07:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:07:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300007.i6U07IUv021549@pub.open-bio.org> mwilkinson Thu Jul 29 20:07:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv21507/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: the adaptor now writes to a new field in the database - signatureURL - which is where Nina's agent expects to find the RDF corresponding to the service. This can be null, if you want to temporarily register a service. moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/26 17:09:09 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:07:18 1.4 @@ -204,7 +204,7 @@ my ($self, %args) = @_; my $dbh = $self->dbh; - $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, + $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description, signatureURL) values (?,?,?,?,?,?,?,?,?)}, undef, $args{'category'}, $args{'servicename'}, @@ -213,7 +213,8 @@ $args{'url'}, $args{'contact_email'}, $args{'authoritative'}, - $args{'description'}); + $args{'description'}, + $args{'signatureURL'}); my $id = $dbh->{mysql_insertid}; return $id; From mwilkinson at pub.open-bio.org Thu Jul 29 20:07:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:07:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300007.i6U07IXA021530@pub.open-bio.org> mwilkinson Thu Jul 29 20:07:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv21507/MOBY Modified Files: Central.pm service_instance.pm Log Message: the adaptor now writes to a new field in the database - signatureURL - which is where Nina's agent expects to find the RDF corresponding to the service. This can be null, if you want to temporarily register a service. moby-live/Perl/MOBY Central.pm,1.135,1.136 service_instance.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.135 retrieving revision 1.136 diff -u -r1.135 -r1.136 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 23:34:06 1.135 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:07:18 1.136 @@ -1082,11 +1082,12 @@ sub registerService { my ($pkg, $payload) = @_; - my ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARY) = &_registerServicePayload($payload); + my ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARY, $signatureURL) = &_registerServicePayload($payload); $authoritativeService = defined($authoritativeService)?1:0; my $error; $error .="missing serviceName \n" unless defined $serviceName; $error .="missing serviceType \n" unless defined $serviceType; + $error .="missing signatureURL \n" unless defined $signatureURL; $error .="missing authURI \n" unless defined $AuthURI; $error .="missing contactEmail \n" unless defined $contactEmail; return &_error("Malformed authURI - must not have an http:// prefix","") if $AuthURI =~ '[/:]'; @@ -1141,6 +1142,7 @@ contact_email => $contactEmail, authoritative => $authoritativeService, description => $desc, + signatureURL => $signatureURL, ); return &_error("Service registration failed for unknown reasons","") if (!defined $SVC); @@ -1167,13 +1169,10 @@ # this is roundabout, I agree, but it is the most re-usable way to go at # the moment. - my ($si, $reg) = &findService('',' - - + my ($si, $reg) = &findService(''," $AuthURI; $serviceName; - - '); + "); unless ($si){ $SVC->DELETE_THYSELF; return &_error("Registration Failed - newly registered service could not be discovered",""); @@ -1356,13 +1355,15 @@ my $contactEmail = &_nodeTextContent($Object, "contactEmail"); my $authoritativeService = &_nodeTextContent($Object, "authoritativeService"); my $URL = &_nodeTextContent($Object, "URL"); + my $signatureURL = &_nodeTextContent($Object, "signatureURL"); my $desc = &_nodeTextContent($Object, "Description"); my $INPUTS = &_nodeRawContent($Object, "Input"); # returns array ref my $OUTPUTS = &_nodeRawContent($Object, "Output"); # returns array ref my $SECONDARIES = &_nodeRawContent($Object, "secondaryArticles"); # returns array ref - return ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARIES); + return ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARIES, $signatureURL); } + sub _extractObjectTypes { my ($DOM) = @_; # DOM is either a or a article $debug && &_LOG("\n\n\nExtracting object types from \n$DOM \n\n"); @@ -2878,7 +2879,7 @@ my $output=""; my $sth = $dbh->prepare(q{ select - category, url, servicename, service_type_uri, authority_id, description, authoritative, contact_email + category, url, servicename, service_type_uri, authority_id, description, authoritative, contact_email, signatureURL from service_instance where service_instance_id = ?}); my $sth_simple_in = $dbh->prepare("select object_type_uri, namespace_type_uris, article_name from simple_input where service_instance_id=? and collection_input_id IS NULL"); @@ -2896,8 +2897,9 @@ foreach (@ids){ $sth->execute($_); - my ($category, $url, $servicename, $service_type_uri, $authority_id, $desc, $authoritative, $email) = $sth->fetchrow_array; + my ($category, $url, $servicename, $service_type_uri, $authority_id, $desc, $authoritative, $email, $signatureURL) = $sth->fetchrow_array; #print "\n\nAFTER EXECUTE $category, $servicename, $service_type_uri, $authority_id, $desc, $authoritative\n\n"; + $signatureURL ||=""; next unless ($servicename && $authority_id); my $service_type = $OSserv->getServiceCommonName($service_type_uri); my ($authURI) = $dbh->selectrow_array(q{select authority_uri from authority where authority_id=?},undef,$authority_id); @@ -2907,6 +2909,7 @@ $output .= "\t$category\n"; $output .= "\t\n$desc\n\t\n"; $output .= "\t$email\n"; + $output .= "\t$signatureURL\n"; $output .= "\t$url\n"; $output .="\t\n"; $sth_simple_in->execute($_); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/09 00:21:53 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:07:18 1.7 @@ -66,6 +66,7 @@ service_type_uri => [undef, 'read/write'], authority => [undef, 'read/write'], authority_uri => [undef, 'read/write'], + signatureURL => [undef, 'read/write'], url => [undef, 'read/write'], inputs => [undef, 'read/write'], outputs => [undef, 'read/write'], @@ -128,6 +129,12 @@ (defined $val) && ($self->{url} = $val); return $self->{url} } + sub signatureURL{ + my ($self, $val) = @_; + if (defined $val && $self->signatureURL){return undef} + (defined $val) && ($self->{signatureURL} = $val); + return $self->{signatureURL} + } sub contact_email { my ($self, $val) = @_; if (defined $val && $self->contact_email){return undef} @@ -240,7 +247,10 @@ url => $self->url, contact_email => $self->contact_email, authoritative => $self->authoritative, - description => $self->description); + description => $self->description, + signatureURL => $self->signatureURL, + ); + $self->service_instance_id($id); $self->{__exists__} = 1; # this service now exists } else { # if it doesn't exist, and you havne't given me anyting I need to create it, then bail out From mwilkinson at pub.open-bio.org Thu Jul 29 20:14:15 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:14:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300014.i6U0EFkP021656@pub.open-bio.org> mwilkinson Thu Jul 29 20:14:15 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv21637/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: adding the new parameter into the test suite moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.19,1.20 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/12 00:39:37 1.19 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:14:15 1.20 @@ -159,6 +159,7 @@ serviceName => "myfirstservice", serviceType => "Retrieval", authURI => "www.illuminae.com", + signatureURL => "http://www.illuminae.com/somewhere", contactEmail => 'your at mail.address', description => "this is my first service", category => "moby", @@ -182,6 +183,7 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your at mail.address', + signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -198,6 +200,7 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your at mail.address', + signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", From mwilkinson at pub.open-bio.org Thu Jul 29 20:16:32 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:16:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300016.i6U0GWli021724@pub.open-bio.org> mwilkinson Thu Jul 29 20:16:32 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv21705/MOBY/Client Modified Files: Central.pm Log Message: adding the new parameter into the client library moby-live/Perl/MOBY/Client Central.pm,1.77,1.78 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.77 retrieving revision 1.78 diff -u -r1.77 -r1.78 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/29 21:53:54 1.77 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/30 00:16:32 1.78 @@ -706,6 +706,7 @@ my $email = $a{contactEmail}; $email ||=""; my $URL = $a{URL}; $URL ||=""; my $desc = $a{description}; $desc ||=""; + my $signatureURL = $a{signatureURL}; $signatureURL ||=""; my $Category = lc($a{category}); chomp $Category; $Category ||=""; return $self->errorRegXML("Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category") unless (($Category eq 'moby') || ($Category eq 'wsdl')); return $self->errorRegXML("All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary") unless ( @@ -717,6 +718,7 @@ $name $type + $signatureURL $URL $authURI $email"; From mwilkinson at pub.open-bio.org Thu Jul 29 20:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:40:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9Vi021885@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv21862/MOBY Modified Files: Central.pm service_instance.pm Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/MOBY Central.pm,1.136,1.137 service_instance.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.136 retrieving revision 1.137 diff -u -r1.136 -r1.137 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:07:18 1.136 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:40:09 1.137 @@ -1087,7 +1087,7 @@ my $error; $error .="missing serviceName \n" unless defined $serviceName; $error .="missing serviceType \n" unless defined $serviceType; - $error .="missing signatureURL \n" unless defined $signatureURL; +# $error .="missing signatureURL \n" unless defined $signatureURL; $error .="missing authURI \n" unless defined $AuthURI; $error .="missing contactEmail \n" unless defined $contactEmail; return &_error("Malformed authURI - must not have an http:// prefix","") if $AuthURI =~ '[/:]'; @@ -1431,9 +1431,12 @@ return &_error("The service specified by authority=$authURI servicename=$serviceName does not exist in the registry", "") unless (MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI, test => 1)); my $SERVICE = MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI); - my $result = $SERVICE->DELETE_THYSELF; - - if ($result){ + if ($SERVICE->signatureURL){ + return &_error("it is illegal to register a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); + } + + my $result = $SERVICE->DELETE_THYSELF; + if ($result){ return &_success("Service Deregistered Successfully",""); } else { return &_error("Service deletion failed for unknown reasons",""); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:07:18 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:40:09 1.8 @@ -231,6 +231,8 @@ $self->contact_email($existing_service->{'email'}); $self->description($existing_service->{'desc'}); $self->authority($existing_service->{'authURI'}); + $self->signatureURL($existing_service->{'signatureURL'}); + $self->{__exists__} = 1; # this service already existed } elsif (!($existing_service) # if it doesn't exist && (defined $self->category) # and you have given me things I need to create it From mwilkinson at pub.open-bio.org Thu Jul 29 20:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:40:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9gp021924@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv21862/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.20,1.21 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:14:15 1.20 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:40:09 1.21 @@ -1,7 +1,7 @@ #!/usr/bin/perl -w use MOBY::Client::Central; -my $v = 1 if ($ARGV[0] eq "verbose"); +my $v = 1 if ($ARGV[0] && ($ARGV[0] eq "verbose")); sub TEST { # test of Registration object ($reg, $test, $expect) = @_; From mwilkinson at pub.open-bio.org Thu Jul 29 20:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:40:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9qT021904@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv21862/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:07:18 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:40:09 1.5 @@ -169,7 +169,7 @@ my ($self, %args) = @_; my $dbh = $self->dbh; - my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? + my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc, $signatureURL) = $dbh->selectrow_array( # does this service already exist? q{select service_instance_id, category, @@ -179,7 +179,8 @@ url, service_instance.contact_email, authoritative, - description + description, + signatureURL from service_instance, authority where service_instance.authority_id = authority.authority_id From mwilkinson at pub.open-bio.org Thu Jul 29 21:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 21:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1EiwK022137@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv22099/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:40:09 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 01:14:44 1.6 @@ -193,6 +193,7 @@ name => $name, servcetype => $typeURI, authURI => $authURI, + signatureURL => $signatureURL, url => $url, email => $email, authoritative => $authoritative, From mwilkinson at pub.open-bio.org Thu Jul 29 21:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 21:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1Eium022118@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv22099/MOBY Modified Files: Central.pm Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/MOBY Central.pm,1.137,1.138 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.137 retrieving revision 1.138 diff -u -r1.137 -r1.138 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:40:09 1.137 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 01:14:44 1.138 @@ -1432,7 +1432,7 @@ return &_error("The service specified by authority=$authURI servicename=$serviceName does not exist in the registry", "") unless (MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI, test => 1)); my $SERVICE = MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI); if ($SERVICE->signatureURL){ - return &_error("it is illegal to register a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); + return &_error("it is illegal to deregister a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); } my $result = $SERVICE->DELETE_THYSELF; From mwilkinson at pub.open-bio.org Thu Jul 29 21:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 21:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1EixZ022157@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv22099/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.21,1.22 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:40:09 1.21 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 01:14:44 1.22 @@ -159,7 +159,6 @@ serviceName => "myfirstservice", serviceType => "Retrieval", authURI => "www.illuminae.com", - signatureURL => "http://www.illuminae.com/somewhere", contactEmail => 'your at mail.address', description => "this is my first service", category => "moby", @@ -183,7 +182,6 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your at mail.address', - signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -200,7 +198,6 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your at mail.address', - signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -266,10 +263,14 @@ serviceName => "myfirstservice", authURI => "www.illuminae.com", ), 28, 1); - -TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 28, 1); -TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 29, 1); -TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 30, 1); +#TEST($C->deregisterService( +# serviceName => "getDragonSimpleAnnotatedImages", +# authURI => "www.illuminae.com", +# ), 29, 0); # cant deregister a service with a signatureURL + +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 30, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 31, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 32, 1); exit 0; From gordonp at pub.open-bio.org Wed Jul 7 16:02:48 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed, 7 Jul 2004 12:02:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071602.i67G2mnT032210@pub.open-bio.org> gordonp Wed Jul 7 12:02:47 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32166/shared Modified Files: MobyPrefixResolver.java Log Message: Fixed issues with SOAP payload parsing related to namespaces and encoding schemes, works with Axis 1.1beta without warnings too moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2004/07/07 16:02:47 1.2 @@ -21,9 +21,13 @@ public class MobyPrefixResolver implements PrefixResolver{ public static final String MOBY_XML_NAMESPACE = "http://www.biomoby.org/moby"; public static final String MOBY_XML_PREFIX = "moby"; + public static final String MOBY_TRANSPORT_NAMESPACE = "http://biomoby.org/"; + public static final String MOBY_TRANSPORT_PREFIX = "mobyt"; public static final String XSI_NAMESPACE1999 = "http://www.w3.org/1999/XMLSchema-instance"; public static final String XSI_NAMESPACE2001 = "http://www.w3.org/2001/XMLSchema-instance"; public static final String XSI_PREFIX = "xsi"; + public static final String XSI1999_PREFIX = "xsi1999"; + public static final String XSI2001_PREFIX = "xsi2001"; /** * We don't really implement this as it can be extremely complicated. @@ -57,8 +61,17 @@ else if(MOBY_XML_PREFIX.equals(prefix)){ return MOBY_XML_NAMESPACE; } + else if(MOBY_TRANSPORT_PREFIX.equals(prefix)){ + return MOBY_TRANSPORT_NAMESPACE; + } else if(XSI_PREFIX.equals(prefix)){ - return XSI_NAMESPACE1999; //Crappy Perl XML Schema namespace usage is out of date + return XSI_NAMESPACE1999; //Crappy Perl XML Schema namespace usage is out of date, use it by default + } + else if(XSI1999_PREFIX.equals(prefix)){ + return XSI_NAMESPACE1999; + } + else if(XSI2001_PREFIX.equals(prefix)){ + return XSI_NAMESPACE2001; //Used by Axis } else{ return ""; // Indicates that we don't have a mapping for this prefix From gordonp at pub.open-bio.org Wed Jul 7 16:02:48 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed, 7 Jul 2004 12:02:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071602.i67G2mxp032191@pub.open-bio.org> gordonp Wed Jul 7 12:02:47 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32166/client Modified Files: MobyRequest.java Log Message: Fixed issues with SOAP payload parsing related to namespaces and encoding schemes, works with Axis 1.1beta without warnings too moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/05/20 16:08:05 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/07/07 16:02:47 1.4 @@ -16,9 +16,7 @@ import javax.xml.parsers.ParserConfigurationException; import javax.xml.transform.TransformerException; import javax.xml.namespace.QName; -import org.w3c.dom.Document; -import org.w3c.dom.Node; -import org.w3c.dom.Element; +import org.w3c.dom.*; // Utilities import java.util.Hashtable; @@ -34,6 +32,7 @@ import org.w3c.dom.NodeList; import org.apache.axis.message.MessageElement; import java.io.PrintStream; +import java.io.StringBufferInputStream; /** * This class handles the WSDL transaction to request a response @@ -56,6 +55,7 @@ protected MobyDataSecondaryInstance[] secondaryData = null; protected Vector outputData = null; protected Central mobyCentral = null; + protected PrefixResolver mobyPrefixResolver = null; protected Hashtable wsdlCache = null; protected String lastWsdlCacheKey = null; @@ -69,6 +69,7 @@ protected XPathContext xpath_context; protected String responseString = null; + private XPath stringEncodedXPath; private XPath base64EncodedXPath; private XPath queryResponseXPath; private XPath simpleChildXPath; @@ -97,11 +98,20 @@ } xpath_context = new XPathContext(); - PrefixResolver mobyPrefixResolver = new MobyPrefixResolver(); + mobyPrefixResolver = new MobyPrefixResolver(); // Now compile the XPath statements that will be used fetch data from the server response try{ - base64EncodedXPath = new XPath("//*[@xsi:type=\"SOAP-ENC:base64\"]", null, mobyPrefixResolver, XPath.SELECT); + base64EncodedXPath = new XPath("//*[starts-with(substring-after(@"+ + MobyPrefixResolver.XSI1999_PREFIX+ + ":type, ':'), \"base64\") or starts-with(substring-after(@"+ + MobyPrefixResolver.XSI2001_PREFIX+ + ":type, ':'), \"base64\")]", null, mobyPrefixResolver, XPath.SELECT); + stringEncodedXPath = new XPath("//*[substring-after(@"+ + MobyPrefixResolver.XSI1999_PREFIX+ + ":type, ':')=\"string\" or substring-after(@"+ + MobyPrefixResolver.XSI2001_PREFIX+ + ":type, ':')=\"string\"]", null, mobyPrefixResolver, XPath.SELECT); queryResponseXPath = new XPath("//moby:mobyData | //mobyData", null, mobyPrefixResolver, XPath.SELECT); simpleChildXPath = new XPath("moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT); collectionChildXPath = new XPath("moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT); @@ -306,23 +316,25 @@ // Should initialize endpoint, etc. This call is AXIS SPECIFIC, otherwise you'll // have to do the call's info setting manually. //((org.apache.axis.client.Call) soapCall).setSOAPService(soapService); - soapCall.setPortTypeName(new QName("http://biomoby.org/", - mobyService.getName() + "PortType")); - soapCall.setOperationName(new QName("http://biomoby.org/", - mobyService.getName())); + soapCall.removeAllParameters(); soapCall.setTargetEndpointAddress(mobyService.getURL()); + soapCall.setPortName(new QName("http://biomoby.org/", + mobyService.getName() + "PortType")); + //soapCall.setOperationName(new QName("http://biomoby.org/", + // mobyService.getName())); soapCall.setSOAPActionURI("http://biomoby.org/#" + mobyService.getName()); - soapCall.setReturnType(XMLType.SOAP_STRING); - soapCall.removeAllParameters(); MobyData[] requiredInputData = mobyService.getPrimaryInputs(); if(requiredInputData == null) return; // A method requiring no input? else{ // There is one argument, the MOBY request object string - soapCall.addParameter("MOBYRequest", - XMLType.SOAP_STRING, - stringType, - ParameterMode.IN); + /*soapCall.setReturnType(new QName("http://biomoby.org/", mobyService.getName())); + soapCall.addParameter("MOBYRequest", + XMLType.SOAP_STRING, + stringType, + ParameterMode.IN);*/ + if(debug) + debugPS.println("Set returnType after addParameter was " + soapCall.getReturnType()); } return; } @@ -337,9 +349,12 @@ //Setup mobyXMLInputData[0] = mobyInputXML; + if(debug) + debugPS.println("returnType just before invoke call is " + soapCall.getReturnType()); Object returnedObject = null; try{ - returnedObject = soapCall.invoke(mobyXMLInputData); + returnedObject = soapCall.invoke(new QName("http://biomoby.org/", + mobyService.getName()), mobyXMLInputData); } catch(Exception e){ throw new SOAPException("While invoking SOAP Call: " + e); @@ -354,6 +369,7 @@ return decodeSOAPMessage(resultDom); //return resultDom; } catch(Exception e){ + e.printStackTrace(); throw new SOAPException("Could not get SOAP response as DOM Element: "+ e); } @@ -368,53 +384,143 @@ * @return The root element of the MOBY response DOM */ protected Element decodeSOAPMessage(Element n) throws SOAPException, MobyException{ - if(n == null){ throw new SOAPException("SOAP Message given to decode is null"); } - // Find base64 encoded elements in the SOAP message using XPath NodeList node_list = null; + Node responseNode = null; + XPath responseElementXPath = null; try{ - node_list = runXPath(base64EncodedXPath, n); + responseElementXPath = new XPath("//"+ MobyPrefixResolver.MOBY_TRANSPORT_PREFIX+ + ":"+mobyService.getName()+"Response", + null, mobyPrefixResolver, XPath.SELECT); }catch(TransformerException te){ throw new SOAPException("Cannot select SOAP nodes due to exception "+ + "while compiling XPath statement (code bug?):" +te); + } + try{ + node_list = runXPath(responseElementXPath, n); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select SOAP nodes due to exception "+ "while executing XPath statement:" +te); } if(node_list == null || node_list.getLength() == 0){ - // Note: before giving up we should really have a plain string check as per the MOBY API 0.6 - throw new SOAPException("Could not find a Base64 encoded SOAP payload"); + throw new SOAPException("Could not find a response element in SOAP payload"); } - // Do decoding for each part found - for(int i = 0; i < node_list.getLength(); i++){ - + + if(node_list.getLength() > 1){ + throw new SOAPException("Found more than one response element in SOAP payload, " + + "unable to resolve ambiguity of the payload (service provider error?)"); + } + responseNode = node_list.item(0); + + // Find base64 encoded elements in the SOAP message using XPath and + // replace them with the real decoded contents + node_list = null; + try{ + node_list = runXPath(base64EncodedXPath, responseNode); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select base64 encoded SOAP nodes due to exception "+ + "while executing XPath statement:" +te); + } + if(debug && node_list != null){ + debugPS.println("There were " + node_list.getLength() + + " base64 encoded elements in the data"); + } + + // Do decoding for each base64 part found + for(int i = 0; node_list != null && i < node_list.getLength(); i++){ org.w3c.dom.Node change = node_list.item(i); - change.normalize(); + /* Make sure the text data is all put into one contiguous piece for decoding*/ + change.normalize(); + byte[] decodedBytes = org.apache.axis.encoding.Base64.decode(change.getFirstChild().getNodeValue()); String newText = new String(decodedBytes); if(debug){ debugPS.println("New decoded text is" + newText); } - // release resources related to the Xpath execution, since we won't be using this doc anymore - releaseXPath(n); - - responseString = new String(decodedBytes); - // Parse the MOBY XML document payload - Document domDoc = null; - try{ - domDoc = docBuilder.parse(new ByteArrayInputStream(decodedBytes)); - } catch(org.xml.sax.SAXException saxe){ - throw new MobyException("The SOAP payload defining the MOBY Result " + - "could not be parsed: " + saxe); - } catch(java.io.IOException ioe){ - throw new MobyException("The SOAP payload defining the MOBY Result " + - " could not be read (from a String!)" + ioe); + // Swap out this node for the decoded data + change.getParentNode().replaceChild(n.getOwnerDocument().createTextNode(new String(decodedBytes)), + change); + } + + // Now see if there are any strings that need decoding + node_list = null; + try{ + node_list = runXPath(stringEncodedXPath, responseNode); + } + catch(TransformerException te){ + throw new SOAPException("Cannot select base64 encoded SOAP nodes due to exception "+ + "while executing XPath statement:" +te); + } + + // Do decoding for each base64 part found + for(int i = 0; node_list != null && i < node_list.getLength(); i++){ + org.w3c.dom.Node change = node_list.item(i); + /* Make sure the text data is all put into one contiguous piece for decoding*/ + change.normalize(); + String plainString = ""; + int j = 0; + for(NodeList children = change.getChildNodes(); + children != null && j < children.getLength(); + j++){ + Node child = children.item(j); + if(child instanceof CDATASection || child instanceof Text){ + plainString += child.getNodeValue(); + } + } + + // Swap out this node for the decoded data + change.getParentNode().replaceChild(n.getOwnerDocument().createTextNode(plainString), change); + } + if(debug && node_list != null){ + debugPS.println("There were " + node_list.getLength() + + " XML Schema string encoded elements in the data"); + } + + // Parse the MOBY XML document payload + responseNode.normalize(); + NodeList children = responseNode.getChildNodes(); + if(children == null){ + throw new MobyException("The MOBY payload has no contents at all"); + } + if(children.getLength() != 1){ + debugPS.println("Warning: MOBY Payload appears to have more than " + + "just text in it, skipping the non-text sections"); + } + + responseString = ""; + for(int j = 0; j < children.getLength(); j++){ + Node child = children.item(j); + if(child instanceof CDATASection || child instanceof Text){ + responseString += child.getNodeValue(); } - return domDoc.getDocumentElement(); } - return null; //Shouldn't get here + + if(responseString.length() == 0){ + throw new MobyException("The MOBY payload has no text contents at all"); + } + + Document domDoc = null; + try{ + domDoc = docBuilder.parse(new StringBufferInputStream(responseString)); + } catch(org.xml.sax.SAXException saxe){ + throw new MobyException("The SOAP payload defining the MOBY Result " + + "could not be parsed: " + saxe); + } catch(java.io.IOException ioe){ + throw new MobyException("The SOAP payload defining the MOBY Result " + + " could not be read (from a String!)" + ioe); + } + + // release resources related to the Xpath execution, since we won't be using this doc anymore + releaseXPath(n); + + return domDoc.getDocumentElement(); } @@ -492,7 +598,7 @@ if(debug){ debugPS.println("Aha! Got " + response_list.getLength() + " mobyContent response elements"); } - // Do data deserialization for each response's mobyData + // Do data decoding for each response's mobyData for(int i = 0; i < response_list.getLength(); i++){ Node response = response_list.item(i); From gordonp at pub.open-bio.org Wed Jul 7 16:07:47 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Wed, 7 Jul 2004 12:07:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407071607.i67G7ln4032248@pub.open-bio.org> gordonp Wed Jul 7 12:07:46 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv32223 Modified Files: ChangeLog Log Message: Recorded fixes to MOBYRequest moby-live/Java/docs ChangeLog,1.15,1.16 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/05/20 16:23:15 1.15 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/07/07 16:07:46 1.16 @@ -1,3 +1,9 @@ +2004-07-07 Paul Gordon + + * Modifications to MobyRequest to handle Axis 1.1beta, and a variety of + encoding schemes (base64 and XSD string) and namespaces (1999 and 2001 + XSD, MOBY transport) + 2004-05-20 Paul Gordon * Added full working example of service discovery and invocation in From mwilkinson at pub.open-bio.org Fri Jul 9 00:21:53 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 20:21:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690LrIk005683@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY/Adaptor/moby Modified Files: queryapi.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/06/24 22:32:39 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/07/09 00:21:53 1.2 @@ -16,12 +16,7 @@ dbname => [undef, 'read/write'], port => [undef, 'read/write'], proxy => [undef, 'read/write'], - sourcetype => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], - url => [undef, 'read/write'], - _implementation => [undef, 'read/write'], # this is the implementation of the API, e.g. mysql - - dbh => [undef, 'read/write'], # once all the calls are converttd remove this! It should not be accessible from outside!!! - + url => [undef, 'read/write'], ); #_____________________________________________________________ @@ -41,10 +36,56 @@ } # List of names of all specified object attributes - sub _standard_keys { + sub _standard_keys_a { keys %_attr_data; } + sub username { + my ($self, $arg) = @_; + $self->{username} = $arg if defined $arg; + return $self->{username}; + } + sub password { + my ($self, $arg) = @_; + $self->{password} = $arg if defined $arg; + return $self->{password}; + } + sub dbname { + my ($self, $arg) = @_; + $self->{dbname} = $arg if defined $arg; + return $self->{dbname}; + } + sub port { + my ($self, $arg) = @_; + $self->{port} = $arg if defined $arg; + return $self->{port}; + } + sub proxy { + my ($self, $arg) = @_; + $self->{proxy} = $arg if defined $arg; + return $self->{proxy}; + } + sub sourcetype { + my ($self, $arg) = @_; + $self->{sourcetype} = $arg if defined $arg; + return $self->{sourcetype}; + } + sub url { + my ($self, $arg) = @_; + $self->{url} = $arg if defined $arg; + return $self->{url}; + } + sub _implementation { + my ($self, $arg) = @_; + $self->{'_implementation'} = $arg if defined $arg; + return $self->{'_implementation'}; + } + sub dbh { + my ($self, $arg) = @_; + $self->{dbh} = $arg if defined $arg; + return $self->{dbh}; + } + } sub new { @@ -54,7 +95,7 @@ my $self = bless {}, $class; - foreach my $attrname ( $self->_standard_keys ) { + foreach my $attrname ( $self->_standard_keys_a ) { if (exists $args{$attrname} && defined $args{$attrname}) { $self->{$attrname} = $args{$attrname} } elsif ($caller_is_obj) { @@ -62,95 +103,88 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - - my $source = $self->sourcetype; - my $datasource = $source->new(adaptor => $self); - unless ($datasource) { - print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; - return undef; - } - $self->_implementation($datasource); - - # the lines below should be removed, since this should be pushed down into the implementation - ############################################################## - unless ($datasource->dbh) { - print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; - return undef; - } - - $self->dbh($datasource->dbh); - ############################################################# - return $self; } sub insert_collection_input { - my ($self, %args) = @_; - my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ - # this should be dropped down into the mysql.pm module?? probably... - $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); - my $id=$self->dbh->{mysql_insertid}; - return $id; - } + die "insert_collection_input not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + #if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # # this should be dropped down into the mysql.pm module?? probably... + # $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + # my $id=$self->dbh->{mysql_insertid}; + # return $id; + #} } sub insert_collection_output { - my ($self, %args) = @_; - my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ - # this should be dropped down into the mysql.pm module?? probably... - $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); - my $id=$self->dbh->{mysql_insertid}; - return $id; - } + die "insert_collection_output not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + #if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # # this should be dropped down into the mysql.pm module?? probably... + # $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + # my $id=$self->dbh->{mysql_insertid}; + # return $id; + #} } sub insert_simple_input { - my ($self, %args) = @_; - my $dbh = $self->dbh; - - $dbh->do("insert into simple_input - (object_type_uri, - namespace_type_uris, - article_name, - service_instance_id, - collection_input_id) - values (?,?,?,?,?)", - undef, - ($args{object_type_uri}, - $args{namespace_type_uris}, - $args{article_name}, - $args{service_instance_id}, - $args{collection_input_id})); - my $id=$dbh->{mysql_insertid}; - return $id; + die "insert_simple_input not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + # + #$dbh->do("insert into simple_input + # (object_type_uri, + # namespace_type_uris, + # article_name, + # service_instance_id, + # collection_input_id) + # values (?,?,?,?,?)", + # undef, + # ($args{object_type_uri}, + # $args{namespace_type_uris}, + # $args{article_name}, + # $args{service_instance_id}, + # $args{collection_input_id})); + #my $id=$dbh->{mysql_insertid}; + #return $id; } sub insert_simple_output { - my ($self, %args) = @_; - my $dbh = $self->dbh; - - $dbh->do("insert into simple_output - (object_type_uri, - namespace_type_uris, - article_name, - service_instance_id, - collection_output_id) - values (?,?,?,?,?)", - undef, - ($args{object_type_uri}, - $args{namespace_type_uris}, - $args{article_name}, - $args{service_instance_id}, - $args{collection_output_id})); - my $id=$dbh->{mysql_insertid}; - return $id; + die "insert_simple_output not implemented in adaptor\n"; + #my ($self, %args) = @_; + #my $dbh = $self->dbh; + # + #$dbh->do("insert into simple_output + # (object_type_uri, + # namespace_type_uris, + # article_name, + # service_instance_id, + # collection_output_id) + # values (?,?,?,?,?)", + # undef, + # ($args{object_type_uri}, + # $args{namespace_type_uris}, + # $args{article_name}, + # $args{service_instance_id}, + # $args{collection_output_id})); + #my $id=$dbh->{mysql_insertid}; + #return $id; } +sub query_service_instance { + die "query_service_instance not implemented in adaptor\n"; +} + +sub insert_service_instance { + die "insert_service_instance not implemented in adaptor\n"; +} + sub _dump { my ($self) = @_; @@ -160,37 +194,37 @@ } sub DESTROY {} - -sub AUTOLOAD { - no strict "refs"; - my ($self, $newval) = @_; - - $AUTOLOAD =~ /.*::(\w+)/; - - my $attr=$1; - if ($self->_accessible($attr,'write')) { - - *{$AUTOLOAD} = sub { - if (defined $_[1]) { $_[0]->{$attr} = $_[1] } - return $_[0]->{$attr}; - }; ### end of created subroutine - -### this is called first time only - if (defined $newval) { - $self->{$attr} = $newval - } - return $self->{$attr}; - - } elsif ($self->_accessible($attr,'read')) { - - *{$AUTOLOAD} = sub { - return $_[0]->{$attr} }; ### end of created subroutine - return $self->{$attr} } - - - # Must have been a mistake then... - croak "No such method: $AUTOLOAD"; -} - +# +#sub AUTOLOAD { +# no strict "refs"; +# my ($self, $newval) = @_; +# +# $AUTOLOAD =~ /.*::(\w+)/; +# +# my $attr=$1; +# if ($self->_accessible($attr,'write')) { +# +# *{$AUTOLOAD} = sub { +# if (defined $_[1]) { $_[0]->{$attr} = $_[1] } +# return $_[0]->{$attr}; +# }; ### end of created subroutine +# +#### this is called first time only +# if (defined $newval) { +# $self->{$attr} = $newval +# } +# return $self->{$attr}; +# +# } elsif ($self->_accessible($attr,'read')) { +# +# *{$AUTOLOAD} = sub { +# return $_[0]->{$attr} }; ### end of created subroutine +# return $self->{$attr} } +# +# +# # Must have been a mistake then... +# croak "No such method: $AUTOLOAD"; +#} +# 1; From mwilkinson at pub.open-bio.org Fri Jul 9 00:21:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 20:21:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690Lshx005702@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/06/24 22:32:39 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/09 00:21:53 1.2 @@ -1,8 +1,13 @@ package MOBY::Adaptor::moby::queryapi::mysql; use strict; -use vars qw($AUTOLOAD); +use vars qw($AUTOLOAD @ISA); use Carp; +use MOBY::Adaptor::moby::queryapi; +use DBI; +use DBD::mysql; + + at ISA = qw{MOBY::Adaptor::moby::queryapi}; # implements the interface { #Encapsulated class data @@ -12,7 +17,6 @@ my %_attr_data = # DEFAULT ACCESSIBILITY ( driver => ["DBI:mysql", 'read/write'], - adaptor => [undef, 'read/write'], # I think this causes a circular reference... dbh => [undef, 'read/write'], ); @@ -38,15 +42,26 @@ keys %_attr_data; } + sub driver { + my ($self, $arg) = @_; + $self->{driver} = $arg if defined $arg; + return $self->{driver}; + } + sub dbh { + my ($self, $arg) = @_; + $self->{dbh} = $arg if defined $arg; + return $self->{dbh}; + } + } sub new { my ($caller, %args) = @_; + my $self = $caller->SUPER::new(%args); + my $caller_is_obj = ref($caller); my $class = $caller_is_obj || $caller; - my $self = bless {}, $class; - foreach my $attrname ( $self->_standard_keys ) { if (exists $args{$attrname} && defined $args{$attrname}) { $self->{$attrname} = $args{$attrname} } @@ -55,58 +70,194 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - + return unless $self->driver; - my $driver = $self->driver; - my $username = $self->adaptor->username; - my $password = $self->adaptor->password; - my $port = $self->adaptor->port; - my $url = $self->adaptor->url; - my $dbname = $self->adaptor->dbname; + my $driver = $self->driver; # inherited from the adaptorI (queryapi) + my $username = $self->username; + my $password = $self->password; + my $port = $self->port; + my $url = $self->url; + my $dbname = $self->dbname; my ($dsn) = "$driver:$dbname:$url:$port"; - #my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database"; - +# print STDERR "\n\nconnectiung to $driver:$dbname:$url:$port\n\n"; my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database"; - return undef unless $dbh; - $self->dbh($dbh); + + + ############################################################## + unless ($dbh) { + print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n"; + return undef; + } + + $self->dbh($dbh); + ############################################################# + + return undef unless $self->dbh; return $self; } -sub DESTROY {} +sub insert_collection_input { + my ($self, %args) = @_; + my $dbh = $self->dbh; + if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # this should be dropped down into the mysql.pm module?? probably... + $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + my $id=$self->dbh->{mysql_insertid}; + return $id; + } +} -sub AUTOLOAD { - no strict "refs"; - my ($self, $newval) = @_; - - $AUTOLOAD =~ /.*::(\w+)/; - - my $attr=$1; - if ($self->_accessible($attr,'write')) { - - *{$AUTOLOAD} = sub { - if (defined $_[1]) { $_[0]->{$attr} = $_[1] } - return $_[0]->{$attr}; - }; ### end of created subroutine - -### this is called first time only - if (defined $newval) { - $self->{$attr} = $newval +sub insert_collection_output { + my ($self, %args) = @_; + my $dbh = $self->dbh; + if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ + # this should be dropped down into the mysql.pm module?? probably... + $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); + my $id=$self->dbh->{mysql_insertid}; + return $id; } - return $self->{$attr}; +} - } elsif ($self->_accessible($attr,'read')) { +sub insert_simple_input { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do("insert into simple_input + (object_type_uri, + namespace_type_uris, + article_name, + service_instance_id, + collection_input_id) + values (?,?,?,?,?)", + undef, + ($args{object_type_uri}, + $args{namespace_type_uris}, + $args{article_name}, + $args{service_instance_id}, + $args{collection_input_id})); + my $id=$dbh->{mysql_insertid}; + return $id; +} - *{$AUTOLOAD} = sub { - return $_[0]->{$attr} }; ### end of created subroutine - return $self->{$attr} } +sub insert_simple_output { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do("insert into simple_output + (object_type_uri, + namespace_type_uris, + article_name, + service_instance_id, + collection_output_id) + values (?,?,?,?,?)", + undef, + ($args{object_type_uri}, + $args{namespace_type_uris}, + $args{article_name}, + $args{service_instance_id}, + $args{collection_output_id})); + my $id=$dbh->{mysql_insertid}; + return $id; - # Must have been a mistake then... - croak "No such method: $AUTOLOAD"; } +sub query_service_instance { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? + q{select + service_instance_id, + category, + serviceName, + service_type_uri, + authority.authority_uri, + url, + service_instance.contact_email, + authoritative, + description + from service_instance, authority + where + service_instance.authority_id = authority.authority_id + and servicename=? and authority.authority_uri = ? + }, + undef,($args{servicename}, $args{authURI})); + return undef unless $serviceid; + return {serviceid => $serviceid, + category => $category, + name => $name, + servcetype => $typeURI, + authURI => $authURI, + url => $url, + email => $email, + authoritative => $authoritative, + desc => $desc, + }; +} + + +sub insert_service_instance { + my ($self, %args) = @_; + my $dbh = $self->dbh; + + $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, + undef, + $args{'category'}, + $args{'servicename'}, + $args{'service_type_uri'}, + $args{'authority_id'}, + $args{'url'}, + $args{'contact_email'}, + $args{'authoritative'}, + $args{'description'}); + + my $id = $dbh->{mysql_insertid}; + return $id; +} + + + +sub _checkURI { + +# my $uri = "http://www.ics.uci.edu/pub/ietf/uri/#Related"; +#print "$1, $2, $3, $4, $5, $6, $7, $8, $9" if +# $uri =~ m{^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?}; +# +#The license for this recipe is available here. +# +#Discussion: +# +#If the match is successful, a URL such as +# +#http://www.ics.uci.edu/pub/ietf/uri/#Related +# +#will be broken down into the following group match variables: +# +#$1 = http: +#$2 = http +#$3 = //www.ics.uci.edu +#$4 = www.ics.uci.edu +#$5 = /pub/ietf/uri/ +#$6 = +#$7 = +#$8 = #Related +#$9 = Related +# +#In general, this regular expression breaks a URI down into the following parts, +#as defined in the RFC: +# +#scheme = $2 +#authority = $4 +#path = $5 +#query = $7 +#fragment = $9 + +} + +sub DESTROY {} 1; From mwilkinson at pub.open-bio.org Fri Jul 9 00:21:53 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 20:21:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690LrJD005664@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY Modified Files: Central.pm Config.pm dbConfig.pm service_instance.pm Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/MOBY Central.pm,1.131,1.132 Config.pm,1.3,1.4 dbConfig.pm,1.2,1.3 service_instance.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.131 retrieving revision 1.132 diff -u -r1.131 -r1.132 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/06/24 22:32:38 1.131 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/09 00:21:53 1.132 @@ -1942,15 +1942,16 @@ sub retrieveService { my ($pkg, $payload) = @_; + # the payload here is actually the full XML from the findService call above... #return "NOT YET IMPLEMENTED"; - my ($AuthURI, $serviceName) = &_retrieveServicePayload($payload); + my ($AuthURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML) = &_retrieveServicePayload($payload); unless ($AuthURI && $serviceName){return ""} my $SI = MOBY::service_instance->new(authority_uri => $AuthURI, servicename => $serviceName); my $wsdls; return "" unless ($SI); if ($SI->category eq 'moby'){ - my $wsdl = &_getServiceWSDL($SI); + my $wsdl = &_getServiceWSDL($SI, $InputXML, $OutputXML, $SecondaryXML); if ($wsdl){ $wsdls .= "\n"; } @@ -1976,7 +1977,27 @@ $serviceName = $x->item($n)->getAttributeNode("serviceName"); # may or may not have a name if ($serviceName){$serviceName = $serviceName->getValue()} } - return ($authURI, $serviceName); + + my $INPUT = $doc->getElementsByTagName("Input"); + my $InputXML = ""; + if ($INPUT->item(0)){ + $InputXML = $INPUT->item(0)->toString; + } + + my $OUTPUT = $doc->getElementsByTagName("Output"); + my $OutputXML = ""; + if ($OUTPUT->item(0)){ + $OutputXML = $OUTPUT->item(0)->toString; + } + + my $SECONDARY = $doc->getElementsByTagName("Output"); + my $SecondaryXML = ""; + if ($SECONDARY->item(0)){ + $SecondaryXML = $SECONDARY->item(0)->toString; + } + + return ($authURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML); + } @@ -2571,7 +2592,7 @@ sub _getServiceWSDL { - my ($SI) = @_; + my ($SI, $InputXML, $OutputXML, $SecondaryXML) = @_; # the lines below causes no end of grief. It is now in a variable. #open (WSDL, "./MOBY/Central_WSDL_SandR.wsdl") || die "can't open WSDL file for search and replace\n"; #my $wsdl = join "", (); @@ -2586,8 +2607,13 @@ my $URL = $SI->url; my $IN = "NOT_YET_DEFINED_INPUTS"; my $OUT = "NOT_YET_DEFINED_OUTPUTS"; - my $INxsd = ""; - my $OUTxsd=""; + + my $INxsd = &_getInputXSD($InputXML, $SecondaryXML); + my $OUTxsd = &_getOutputXSD($OutputXML); + + $INxsd ||= ""; + $OUTxsd ||=""; + $wsdl =~ s/MOBY__SERVICE__NAME__/$serviceName/g; # replace all of the goofy portbindingpottype crap $wsdl =~ s/\<\!\-\-\s*MOBY__SERVICE__DESCRIPTION\s*\-\-\>/Authority: $AuthURI - $desc/g; # add a sensible description $wsdl =~ s/MOBY__SERVICE__URL/$URL/g; # the URL to the service @@ -3045,6 +3071,125 @@ END +=head2 _getInputXSD + + name : _getInputXSD($InputXML, $SecondaryXML) + function: to get an XSD describing the input to a MOBY Service, + e.g. to use in a WSDL document + args : (see _serviceListResponse code above for full details of XML) + $InputXML - the ... block of a findService + response message + + $SecondaryXML - the ... + fragment of a findService response message + + returns : XSD fragment of XML (should not return an XML header!) + notes : the structure of an Input block is as follows: + + + + + the structure of a secondaryArticle block is as follows: + + + + + +=over + +=item * Simple + + + ObjectOntologyTerm + NamespaceTerm + ... + + +=item * Collection note that articleName of the contained Simple objects is not required, and is ignored. + + + + ...... + ...... + + +=item * Secondary + + + + INT|FLOAT|STRING + ... + ... + ... + ... + ... + + +=back + +=cut + + +sub _getInputXSD { + my ($Input, $Secondary) =@_; + my $XSD; + + + return $XSD; +} + +=head2 _getOuputXSD + + name : _getOutputXSD($OutputXML) + function: to get an XSD describing the output from a MOBY Service + e.g. to use in a WSDL document + args : (see _serviceListResponse code above for full details) + $InputXML - the ... block of a findService + response message + + $SecondaryXML - the ... + fragment of a findService response message + + returns : XSD fragment of XML (should not return an XML header!) + notes : the structure of an Output block is as follows: + + + + +=over + +=item * Simple + + + ObjectOntologyTerm + NamespaceTerm + ... + + +=item * Collection note that articleName of the contained Simple objects is not required, and is ignored. + + + + ...... + ...... + + +=back + +=cut + +sub _getOutputXSD { + my ($Output) =@_; + my $XSD; + + + return $XSD; +} + 1; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/06/24 22:32:38 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/07/09 00:21:53 1.4 @@ -74,7 +74,7 @@ } my $file = $ENV{MOBY_CENTRAL_CONFIG}; - $file || die "can't open MOBY Configuration file $!\n"; + (-e $file) || die "can't open MOBY Configuration file $!\n"; chomp $file; if ((-e $file) && (!(-d $file))){ @@ -106,27 +106,22 @@ if ($self->{"${source}Adaptor"}){return $self->{"${source}Adaptor"}}; # read from cache - my $username = $self->$source->{username}; # $self->source returns a MOBY::dbConfig object + my $username = $self->$source->{username}; # $self->$source returns a MOBY::dbConfig object my $password = $self->$source->{password}; my $port = $self->$source->{port}; my $dbname = $self->$source->{dbname}; my $url = $self->$source->{url}; my $adaptor = $self->$source->{adaptor}; - my $sourcetype = $self->$source->{sourcetype}; eval "require $adaptor"; return undef if $@; - eval "require $sourcetype"; - return undef if $@; - my $ADAPTOR = $adaptor->new( # by default, this is queryapi - source => $source, + my $ADAPTOR = $adaptor->new( # by default, this is queryapi::mysql username => $username, password => $password, port => $port, dbname => $dbname, url => $url, - sourcetype => $sourcetype, ); if ($ADAPTOR){ $self->{"${source}Adaptor"} = $ADAPTOR; # cache it =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm 2004/06/29 16:23:59 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm 2004/07/09 00:21:53 1.3 @@ -18,8 +18,7 @@ dbname => [undef, 'read/write'], port => [undef, 'read/write'], proxy => [undef, 'read/write'], - adaptor => ["MOBY::Adaptor::moby::queryapi", 'read/write'], - sourcetype => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], + adaptor => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'], url => [undef, 'read/write'], section => [undef, 'read/write'], ); @@ -44,7 +43,7 @@ sub _standard_keys { keys %_attr_data; } - # List of names of all specified object attributes + sub database_title { my ($self, $val) = @_; $self->section_title($val) if $val; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/06/24 22:32:38 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/09 00:21:53 1.6 @@ -8,6 +8,7 @@ use MOBY::central_db_connection; use MOBY::OntologyServer; use MOBY::authority; +use MOBY::Config; #@ISA = qw(MOBY::central_db_connection); # can't do this yet... @@ -74,14 +75,6 @@ description => [undef, 'read/write'], registry => ['MOBY_Central', 'read/write'], test => [0, 'read/write'], # toggles create or test_existence behaviour - - username => ["mobycentral", 'read/write'], - password => ["mobycentral", 'read/write'], - dbname => ["mobycentral", 'read/write'], - host => ["localhost", 'read/write'], - port => [3306, 'read/write'], - dbh => [undef, 'read/write'], - ); #_____________________________________________________________ @@ -147,14 +140,23 @@ (defined $val) && ($self->{description} = $val); return $self->{description} } + + sub dbh { + $CONFIG ||=MOBY::Config->new; # exported by Config.pm + my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral')->dbh; + } + sub adaptor { + $CONFIG ||=MOBY::Config->new; # exported by Config.pm + my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral'); + } } -sub _dbh { - my ($self) = @_; - - my $central_connect = MOBY::central_db_connection->new(); - $self->dbh($central_connect->dbh); -} +#sub _dbh { +# my ($self) = @_; +# +# my $central_connect = MOBY::central_db_connection->new(); +# $self->dbh($central_connect->dbh); +#} sub new { my ($caller, %args) = @_; @@ -186,13 +188,15 @@ return undef unless $self->authority_uri; return undef unless $self->servicename; - $self->_dbh(); - return undef unless $self->dbh; - my $dbh = $self->dbh; + #$self->_dbh(); + #return undef unless $self->dbh; + #my $dbh = $self->dbh; if ($self->test){ return $self->service_instance_exists} - $self->authority($self->_get_authority()); + $self->authority($self->_get_authority()); # this might not be necessary - it simply converts auth_uri to auth_id and v.v.? + # it actually is necessary for the moment. We need to put the logic of determining + # service id into the mysql.pm module!! if ($self->service_type){ my $OE = MOBY::OntologyServer->new(ontology => 'service'); @@ -201,54 +205,43 @@ ($self->service_type =~ /urn:lsid/)?$self->service_type_uri($self->service_type):$self->service_type_uri($servicetypeURI); } - my ($serviceid, $category, $name, $typeURI, $authid,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? - q{select - service_instance_id, - category, - serviceName, - service_type_uri, - authority_id, - url, - contact_email, - authoritative, - description - from service_instance where servicename=? and authority_id=?}, - undef,($self->servicename, $self->authority->authority_id)); + my $existing_service = $self->adaptor->query_service_instance (servicename => $self->servicename, authURI => $self->authority_uri); + + - if ((defined $serviceid) # if it exists, you are not allowed to have passed anything other than service name and authorityURI + if (($existing_service) # if it exists, you are not allowed to have passed anything other than service name and authorityURI && ((defined $self->category) || (defined $self->service_type) || (defined $self->url) || (defined $self->contact_email) || (defined $self->description))){ return -1; # no no no, not alowed to do that! I will not give you an object - } elsif (defined $serviceid){ # if service exists, then instantiate it from the database retrieval we just did - $self->service_instance_id($serviceid); - $self->category($category); - $self->service_type($typeURI); - $self->url($url); - $self->contact_email($email); - $self->description($desc); - $self->authority($self->_get_authority); + } elsif ($existing_service){ # if service exists, then instantiate it from the database retrieval we just did + $self->service_instance_id($existing_service->{'serviceid'}); + $self->category($existing_service->{'category'}); + $self->service_type($existing_service->{'servicetype'}); + $self->url($existing_service->{'url'}); + $self->contact_email($existing_service->{'email'}); + $self->description($existing_service->{'desc'}); + $self->authority($existing_service->{'authURI'}); $self->{__exists__} = 1; # this service already existed - } elsif (!(defined $serviceid) # if it doesn't exist + } elsif (!($existing_service) # if it doesn't exist && (defined $self->category) # and you have given me things I need to create it && (defined $self->service_type) && (defined $self->url) && (defined $self->contact_email) && (defined $self->description)) { # then create it de novo if we have enough information - $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, - undef, - $self->category, - $self->servicename, - $self->service_type_uri, - $self->authority->authority_id, - $self->url, - $self->contact_email, - $self->authoritative, - $self->description); - $self->service_instance_id($dbh->{mysql_insertid}); + my $id = $self->adaptor->insert_service_instance( + category => $self->category, + servicename => $self->servicename, + service_type_uri => $self->service_type_uri, + authority_id => $self->authority_id, + url => $self->url, + contact_email => $self->contact_email, + authoritative => $self->authoritative, + description => $self->description); + $self->service_instance_id($id); $self->{__exists__} = 1; # this service now exists } else { # if it doesn't exist, and you havne't given me anyting I need to create it, then bail out return undef; @@ -263,6 +256,8 @@ unless ($self->{__exists__}){ return undef } + $CONFIG ||=MOBY::Config->new; + $dbh->do(q{delete from service_instance where service_instance_id = ?},undef,$self->service_instance_id); $dbh->do(q{delete from simple_input where service_instance_id = ?},undef,$self->service_instance_id); $dbh->do(q{delete from simple_output where service_instance_id = ?},undef,$self->service_instance_id); @@ -299,7 +294,7 @@ } -sub _get_authority { +sub _get_authority { # there's somethign fishy here... the authority.pm object already knows about authority_id and authorty_uri, doens't it? my ($self) = @_; my $dbh = $self->dbh; my $authority; From mwilkinson at pub.open-bio.org Fri Jul 9 00:21:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 20:21:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090021.i690Lsns005722@pub.open-bio.org> mwilkinson Thu Jul 8 20:21:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv5633/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/06/16 19:07:34 1.17 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/09 00:21:53 1.18 @@ -213,19 +213,33 @@ ["Object", ['UglyNamespace']], # Simple ]), 24, 1); +my ($si, $reg) = $C->findService( + serviceName => "myfirstservice2" +); + +$si = $si->[0]; +my $wsdl = $C->retrieveService($si); +print $wsdl; +if ($wsdl && ($wsdl =~ /\deregisterService( serviceName => "myfirstservice2", authURI => "www.illuminae.com", - ), 25, 1); + ), 26, 1); TEST($C->deregisterService( serviceName => "myfirstservice2", authURI => "www.illuminae.com", - ), 26, 0); + ), 27, 0); TEST($C->deregisterService( serviceName => "myfirstservice", authURI => "www.illuminae.com", - ), 27, 1); + ), 28, 1); TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 28, 1); TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 29, 1); From mwilkinson at pub.open-bio.org Fri Jul 9 02:44:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 8 Jul 2004 22:44:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407090244.i692imAX006132@pub.open-bio.org> mwilkinson Thu Jul 8 22:44:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory pub.open-bio.org:/tmp/cvs-serv6113 Modified Files: LocalServices.pm Log Message: added the Union and Intersection services required by the Generation Challenge Program project. The existing client will not be able to discover nor use these services. moby-live/Perl/scripts/Services LocalServices.pm,1.63,1.64 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v retrieving revision 1.63 retrieving revision 1.64 diff -u -r1.63 -r1.64 --- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2004/06/29 16:24:00 1.63 +++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2004/07/09 02:44:48 1.64 @@ -1031,6 +1031,102 @@ } +sub ObjectUnion { + my ($caller, $data) = @_; # data is raw XML + my $MOBY_RESPONSE; + my $inputs= complexServiceInputParser($data); # thos converts it to XML::DOM objects + # hashref $input->{X} = [[COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]]...] + + return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (keys %{$inputs}); + + foreach my $queryID (keys %{$inputs}){ + my @inputlist = @{$inputs->{$queryID}}; + my $input1 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + my $input2 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + # input1 is now [COLLECTION(1), [DOM1, DOM2]] + my ($type1, $DOMS1) = @{$input1}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + my ($type2, $DOMS2) = @{$input2}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + + unless (($type1 == COLLECTION) && ($type2 == COLLECTION)){ # COLLECTION is a constant exported from MOBY::CommonSubs + $MOBY_RESPONSE .= collectionResponse([], "", $queryID) ; + next; + } + + my @DOMS1 = @{$DOMS1}; + my @DOMS2 = @{$DOMS2}; + my @ALLDOMS = (@DOMS1, @DOMS2); + + my %DOMHASH; + map {$DOMHASH{"$_"} = $_} @ALLDOMS; + + foreach my $dom1(@DOMS1){ + my $ns1 = getSimpleArticleNamespaceURI($dom1); + my ($id1) = getSimpleArticleIDs([$dom1]); + foreach my $dom2(@DOMS2){ + my $ns2 = getSimpleArticleNamespaceURI($dom2); + my ($id2) = getSimpleArticleIDs([$dom2]); + + if (($ns1 eq $ns2) && ($id1 eq $id2)){ + delete $DOMHASH{"$dom2"}; + } + } + } + my @simples; + while (my ($key, $DOM) = each %DOMHASH){ + push @simples, extractRawContent($DOM); + } + $MOBY_RESPONSE .= collectionResponse(\@simples, "UnionCollection", $queryID) ; + + } + #print $MOBY_RESPONSE; +# return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter)); +} + + +sub ObjectIntersection { + my ($caller, $data) = @_; # data is raw XML + my $MOBY_RESPONSE; + my $inputs= complexServiceInputParser($data); # thos converts it to XML::DOM objects + # hashref $input->{X} = [[COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]]...] + + return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (keys %{$inputs}); + + foreach my $queryID (keys %{$inputs}){ + my @inputlist = @{$inputs->{$queryID}}; + my $input1 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + my $input2 = shift @inputlist; # @inputlist = [COLLECTION(1), [DOM1, DOM2]], [COLLECTION(2), [DOM3, DOM4]] + # input1 is now [COLLECTION(1), [DOM1, DOM2]] + my ($type1, $DOMS1) = @{$input1}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + my ($type2, $DOMS2) = @{$input2}; # $type = COLLECTION, $DOMS = [DOM1, DOM2] + + unless (($type1 == COLLECTION) && ($type2 == COLLECTION)){ # COLLECTION is a constant exported from MOBY::CommonSubs + $MOBY_RESPONSE .= collectionResponse([], "", $queryID) ; + next; + } + + my @DOMS1 = @{$DOMS1}; + my @DOMS2 = @{$DOMS2}; + my @gooddoms; + foreach my $dom1(@DOMS1){ + my $ns1 = getSimpleArticleNamespaceURI($dom1); + my ($id1) = getSimpleArticleIDs([$dom1]); + foreach my $dom2(@DOMS2){ + my $ns2 = getSimpleArticleNamespaceURI($dom2); + my ($id2) = getSimpleArticleIDs([$dom2]); + + if (($ns1 eq $ns2) && ($id1 eq $id2)){ + push @gooddoms, extractRawContent($dom1); + } + } + } + $MOBY_RESPONSE .= collectionResponse(\@gooddoms, "IntersectionCollection", $queryID) ; + + } + print $MOBY_RESPONSE; +# return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter)); +} + + ############################################################### ###################### for My Machine Only ################### sub _dbAccess { From mwilkinson at pub.open-bio.org Mon Jul 12 00:39:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun, 11 Jul 2004 20:39:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407120039.i6C0dbuC025484@pub.open-bio.org> mwilkinson Sun Jul 11 20:39:37 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv25446/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: tightening the business logic of MOBY Object registration, as I now see a few objects in the ontology that are invalid. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/09 00:21:53 1.18 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/12 00:39:37 1.19 @@ -1,13 +1,15 @@ #!/usr/bin/perl -w use MOBY::Client::Central; +my $v = 1 if ($ARGV[0] eq "verbose"); + sub TEST { # test of Registration object ($reg, $test, $expect) = @_; die "\a\a\aREG OBJECT MALFORMED" unless $reg; if ($reg->success == $expect){ - print "test $test\t\t[PASS]\n"; + print "test $test\t\t[PASS] ", ($v?($reg->message):""),"\n"; } else { - print "test $test\t\t[FAIL]\n",$reg->message,"\n\n"; + print "test $test\t\t[FAIL] ",$reg->message,"\n\n"; } } sub TEST2 { # test of ServiceInstance object listref @@ -31,8 +33,8 @@ ); -#reg first object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +#register with two ISA's -> should fail +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "blah.blah.blah", @@ -42,35 +44,56 @@ ['Object', 'articleName2']], HASA => [ ['Object', 'articleName3']]} + ), '1a', 0); + +#register with no ISA's -> should fail +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", + description => "a human-readable description of the object", + contactEmail => 'your at email.address', + authURI => "blah.blah.blah", + Relationships => { + HASA => [ + ['Object', 'articleName3']]} + ), '1b', 0); + +#reg first object class with a single ISA -> should pass +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", + description => "a human-readable description of the object", + contactEmail => 'your at email.address', + authURI => "blah.blah.blah", + Relationships => { + ISA => [ + ['Object', 'articleName2']], + HASA => [ + ['Object', 'articleName3']]} ), 1, 1); #reg duplicate object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['Object', 'article1'], - ['Object', 'articleName2']], + ['Object', 'article1'] + ], HASA => [ ['Object', 'articleName3']]} ), 2, 0); #reg second object class -TEST($C->registerObjectClass(objectType => "YetMoreCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject2", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['Object', 'article1'], ['Object', 'articleName2']], HASA => [ ['Object', 'articleName3']]} ), 3, 1); -TEST($C->registerServiceType(serviceType => "CrappyService", +TEST($C->registerServiceType(serviceType => "HypotheticalService1", description => "a human-readable description of the service", contactEmail => 'your at email.address', authURI => "blah.blah.blah", @@ -78,7 +101,7 @@ ISA => ['Retrieval','Analysis']} ), 4, 1); -TEST($C->registerServiceType(serviceType => "CrappyService", +TEST($C->registerServiceType(serviceType => "HypotheticalService1", description => "a human-readable description of the service", contactEmail => 'your at email.address', authURI => "blah.blah.blah", @@ -86,28 +109,28 @@ ISA => ['Retrieval','Analysis']} ), 5, 0); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 6, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 7, 0); -TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 8, 1); -TEST($C->deregisterServiceType(serviceType => "CrappyService"), 9, 1); -TEST($C->deregisterServiceType(serviceType => "CrappyService"), 10, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 6, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 7, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 8, 1); +TEST($C->deregisterServiceType(serviceType => "HypotheticalService1"), 9, 1); +TEST($C->deregisterServiceType(serviceType => "HypotheticalService1"), 10, 0); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your at address.here'), 11, 1); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your at address.here'), 12, 0); -TEST($C->deregisterNamespace(namespaceType =>'UglyNamespace'), 13, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 13, 1); #reg first object class -TEST($C->registerObjectClass(objectType => "TotalCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject1", description => "a human-readable description of the object", - contactEmail => 'your at email.address', + contactEmail => 'your at email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ @@ -115,19 +138,19 @@ ), 14, 1); #reg duplicate object class -TEST($C->registerObjectClass(objectType => "YetMoreCrap", +TEST($C->registerObjectClass(objectType => "HypotheticalObject2", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "blah.blah.blah", Relationships => { ISA => [ - ['TotalCrap', 'article1']]} + ['HypotheticalObject1', 'article1']]} ), 15, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 16, 0); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 16, 0); TEST($C->registerNamespace( - namespaceType =>'UglyNamespace', + namespaceType =>'HypotheticalNamespace1', authURI => 'your.authority.URI', description => "human readable description of namespace", contactEmail => 'your at address.here'), 17, 1); @@ -141,10 +164,10 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ - ['articleName1', [Object => ['UglyNamespace']]], # Simple + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], secondary => { parametername1 => { @@ -163,10 +186,10 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ - ['articleName1', [Object => ['UglyNamespace']]], # Simple + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], ), 19, 0); @@ -179,11 +202,11 @@ category => "moby", URL => "http://illuminae/cgi-bin/service.pl", input =>[ -# ['articleName1', [[Object => ['UglyNamespace']]]], # Collection - ['articleName1', [Object => ['UglyNamespace']]], # Simple +# ['articleName1', [[Object => ['HypotheticalNamespace1']]]], # Collection + ['articleName1', [Object => ['HypotheticalNamespace1']]], # Simple ], output =>[ - ['articleName2', [String => ['UglyNamespace']]], # Simple + ['articleName2', [String => ['HypotheticalNamespace1']]], # Simple ], ), 20, 1); @@ -210,7 +233,7 @@ TEST2($C->findService( input =>[ - ["Object", ['UglyNamespace']], # Simple + ["Object", ['HypotheticalNamespace1']], # Simple ]), 24, 1); my ($si, $reg) = $C->findService( @@ -241,9 +264,9 @@ authURI => "www.illuminae.com", ), 28, 1); -TEST($C->deregisterObjectClass(objectType => "YetMoreCrap"), 28, 1); -TEST($C->deregisterObjectClass(objectType => "TotalCrap"), 29, 1); -TEST($C->deregisterNamespace(namespaceType =>'UglyNamespace'), 30, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 28, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 29, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 30, 1); exit 0; From mwilkinson at pub.open-bio.org Mon Jul 12 00:39:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun, 11 Jul 2004 20:39:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407120039.i6C0dbk6025465@pub.open-bio.org> mwilkinson Sun Jul 11 20:39:37 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv25446/MOBY Modified Files: Central.pm Log Message: tightening the business logic of MOBY Object registration, as I now see a few objects in the ontology that are invalid. moby-live/Perl/MOBY Central.pm,1.132,1.133 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.132 retrieving revision 1.133 diff -u -r1.132 -r1.133 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/09 00:21:53 1.132 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/12 00:39:37 1.133 @@ -260,16 +260,20 @@ return &_error("Object name may not be an URN or URI","") if $1; } + my $ISAs; # validate that the final ontology will be valid by testing against existing relationships and such while (my ($reltype, $obj) = each %{$relationships}){ my ($success, $message, $URI) = $RelOntologyServer->relationshipExists(term => $reltype, ontology => 'object'); # success = 1 if it does - $success==0 && return &_error($message, $URI ); + $success==0 && return &_error($message, $URI ); foreach (@{$obj}){ + ++$ISAs if ($URI =~ /isa$/i); my ($objectType, $articleName) = @{$_}; my ($success, $message, $URI) = $OntologyServer->objectExists(term => $objectType); # success = 1 if it does $success==0 && return &_error($message, $URI ); } } + return &_error("Object must have exactly one ISA parent in the MOBY Object ontology") unless $ISAs == 1; + $clobber = defined($clobber)?$clobber:0; $clobber = 0 unless ($clobber eq 0 || $clobber eq 1 || $clobber eq 2); # safety! my ($exists, $exists_message, $URI) = $OntologyServer->objectExists(term => $term); # success = 1 if it does From gss at pub.open-bio.org Thu Jul 15 20:18:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152018.i6FKI1rq011930@pub.open-bio.org> gss Thu Jul 15 16:18:01 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv11909/S-MOBY/ref-impl/core/src/org/smoby/tools Added Files: ModelRetriever.java Log Message: New class moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools ModelRetriever.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:20:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:20:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152020.i6FKKb1I012013@pub.open-bio.org> gss Thu Jul 15 16:20:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients In directory pub.open-bio.org:/tmp/cvs-serv11988/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients Modified Files: SimpleProviderEngagerPanel.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/05/27 19:37:10 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/15 20:20:37 1.2 @@ -113,11 +113,19 @@ { Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML); MOBYProvider provider = parser.parseProvider(); - String graphURI = provider.getURI(); - HTTPRequest request = HTTPRequest.newPostRequest(graphURI); - request.addParameter("graph", graphString); - HTTPResponse response = request.send(); - outputArea.setText(response.getBody()); + + if (provider == null) + { + outputArea.setText("Couldn't parse provider"); + } + else + { + String graphURI = provider.getURI(); + HTTPRequest request = HTTPRequest.newPostRequest(graphURI); + request.addParameter("graph", graphString); + HTTPResponse response = request.send(); + outputArea.setText(response.getBody()); + } } catch (UnparsableGraphException e) { From gss at pub.open-bio.org Thu Jul 15 20:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQk3E012103@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/.settings Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkwN012085@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkOl012067@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQkuH012123@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQliU012249@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlDU012205@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlHB012225@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlUT012267@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlYq012162@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlxu012184@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQk15012141@pub.open-bio.org> gss Thu Jul 15 16:26:46 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlH1012291@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmbX012374@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQlZA012314@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmBr012332@pub.open-bio.org> gss Thu Jul 15 16:26:47 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmaL012395@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmnC012457@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQm4Q012413@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQo1w012727@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnrV012522@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmSf012480@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnJe012541@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQn4m012564@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpN3012897@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnHE012607@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoG9012649@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQm9p012354@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpEM012918@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQncw012627@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnXG012498@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQos9012668@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpSD012772@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQqtU012963@pub.open-bio.org> gss Thu Jul 15 16:26:52 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQolE012709@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQmF9012436@pub.open-bio.org> gss Thu Jul 15 16:26:48 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpAW012857@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoZp012686@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQp4d012834@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpCE012790@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQnON012586@pub.open-bio.org> gss Thu Jul 15 16:26:49 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQoqc012745@pub.open-bio.org> gss Thu Jul 15 16:26:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQpKD012879@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQp8C012808@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQq1p012983@pub.open-bio.org> gss Thu Jul 15 16:26:52 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:26:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:26:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152026.i6FKQqpi012939@pub.open-bio.org> gss Thu Jul 15 16:26:51 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv12043/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFCk013305@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Added Files: index.html hello-world.n3 n3.html hello-world.rdf engage.html top-frame.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello index.html,NONE,1.1 hello-world.n3,NONE,1.1 n3.html,NONE,1.1 hello-world.rdf,NONE,1.1 engage.html,NONE,1.1 top-frame.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHYE013477@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use Added Files: HTTPException.html HTTPResponse.html HTTPRequest.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http/class-use HTTPException.html,NONE,1.1 HTTPResponse.html,NONE,1.1 HTTPRequest.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGme013365@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util Added Files: RDFXMLSerialization.n3 Serialization.n3 N3Serialization.n3 index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/util RDFXMLSerialization.n3,NONE,1.1 Serialization.n3,NONE,1.1 N3Serialization.n3,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREU4013154@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer Added Files: index.html search.html suggest.html dev-tools.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer index.html,NONE,1.1 search.html,NONE,1.1 suggest.html,NONE,1.1 dev-tools.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRE5o013190@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary Added Files: VocabularyDescription.html package-use.html MOBY.html package-frame.html package-tree.html package-summary.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary VocabularyDescription.html,NONE,1.1 package-use.html,NONE,1.1 MOBY.html,NONE,1.1 package-frame.html,NONE,1.1 package-tree.html,NONE,1.1 package-summary.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFmO013260@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files Added Files: index-7.html index-5.html index-12.html index-16.html index-11.html index-3.html index-1.html index-10.html index-14.html index-4.html index-9.html index-15.html index-8.html index-2.html index-6.html index-13.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/index-files index-7.html,NONE,1.1 index-5.html,NONE,1.1 index-12.html,NONE,1.1 index-16.html,NONE,1.1 index-11.html,NONE,1.1 index-3.html,NONE,1.1 index-1.html,NONE,1.1 index-10.html,NONE,1.1 index-14.html,NONE,1.1 index-4.html,NONE,1.1 index-9.html,NONE,1.1 index-15.html,NONE,1.1 index-8.html,NONE,1.1 index-2.html,NONE,1.1 index-6.html,NONE,1.1 index-13.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREOr013137@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core Added Files: __Collection.n3 Subject.n3 Provider name oneLineDescription.n3 Subject hasMapping.n3 operatesOn Provider.n3 providerAboutURI.n3 __Collection subjectProperty.n3 __NonCollection objectProperty name.n3 subjectProperty Object.n3 keyword.n3 objectProperty.n3 __Bag operatesOn.n3 Graph __NonCollection.n3 keyword __Seq __Alt.n3 __Alt Graph.n3 oneLineDescription mapsTo.n3 __List.n3 mapsTo __Seq.n3 index.html __List providerAboutURI hasMapping __Bag.n3 Object Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies/core __Collection.n3,NONE,1.1 Subject.n3,NONE,1.1 Provider,NONE,1.1 name,NONE,1.1 oneLineDescription.n3,NONE,1.1 Subject,NONE,1.1 hasMapping.n3,NONE,1.1 operatesOn,NONE,1.1 Provider.n3,NONE,1.1 providerAboutURI.n3,NONE,1.1 __Collection,NONE,1.1 subjectProperty.n3,NONE,1.1 __NonCollection,NONE,1.1 objectProperty,NONE,1.1 name.n3,NONE,1.1 subjectProperty,NONE,1.1 Object.n3,NONE,1.1 keyword.n3,NONE,1.1 objectProperty.n3,NONE,1.1 __Bag,NONE,1.1 operatesOn.n3,NONE,1.1 Graph,NONE,1.1 __NonCollection.n3,NONE,1.1 keyword,NONE,1.1 __Seq,NONE,1.1 __Alt.n3,NONE,1.1 __Alt,NONE,1.1 Graph.n3,NONE,1.1 oneLineDescription,NONE,1.1 mapsTo.n3,NONE,1.1 __List.n3,NONE,1.1 mapsTo,NONE,1.1 __Seq.n3,NONE,1.1 index.html,NONE,1.1 __List,NONE,1.1 providerAboutURI,NONE,1.1 hasMapping,NONE,1.1 __Bag.n3,NONE,1.1 Object,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDBM013048@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api Added Files: deprecated-list.html overview-frame.html developer.html constant-values.html allclasses-noframe.html packages.html stylesheet.css allclasses-frame.html package-list help-doc.html serialized-form.html overview-summary.html overview-tree.html index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api deprecated-list.html,NONE,1.1 overview-frame.html,NONE,1.1 developer.html,NONE,1.1 constant-values.html,NONE,1.1 allclasses-noframe.html,NONE,1.1 packages.html,NONE,1.1 stylesheet.css,NONE,1.1 allclasses-frame.html,NONE,1.1 package-list,NONE,1.1 help-doc.html,NONE,1.1 serialized-form.html,NONE,1.1 overview-summary.html,NONE,1.1 overview-tree.html,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRD2P013064@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use Added Files: MOBYDocumentImpl.html MOBYProviderSetImpl.html MOBYDescriptorImpl.html MOBYObjectFactory.html MOBYNonNegativeIntegerConstraintImpl.html MOBYMappingElementImpl.html MOBYProviderImpl.html MOBYDateConstraintImpl.html MOBYNonPositiveIntegerConstraintImpl.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl/class-use MOBYDocumentImpl.html,NONE,1.1 MOBYProviderSetImpl.html,NONE,1.1 MOBYDescriptorImpl.html,NONE,1.1 MOBYObjectFactory.html,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.html,NONE,1.1 MOBYMappingElementImpl.html,NONE,1.1 MOBYProviderImpl.html,NONE,1.1 MOBYDateConstraintImpl.html,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREJE013172@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Added Files: .cvsignore web.xml Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDcJ013101@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use Added Files: MOBYGraph.html MOBYOntology.html MOBYSingleElement.html MOBYObject.html MOBYProviderSet.html MOBYSubject.html MOBYGraphNode.html MOBYMappingElement.html MOBYUnorderedCollection.html MOBYResource.html MOBYEnumeration.html MOBYCollection.html MOBYPropertyValueConstraint.html MOBYDocument.html MOBYLiteral.html MOBYDescriptor.html MOBYPropertyValueException.html MOBYProvider.html MOBYFixedCollection.html MOBYPropertyValue.html MOBYOrderedCollection.html MOBYResizableCollection.html MOBYPropertyValueStatement.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/class-use MOBYGraph.html,NONE,1.1 MOBYOntology.html,NONE,1.1 MOBYSingleElement.html,NONE,1.1 MOBYObject.html,NONE,1.1 MOBYProviderSet.html,NONE,1.1 MOBYSubject.html,NONE,1.1 MOBYGraphNode.html,NONE,1.1 MOBYMappingElement.html,NONE,1.1 MOBYUnorderedCollection.html,NONE,1.1 MOBYResource.html,NONE,1.1 MOBYEnumeration.html,NONE,1.1 MOBYCollection.html,NONE,1.1 MOBYPropertyValueConstraint.html,NONE,1.1 MOBYDocument.html,NONE,1.1 MOBYLiteral.html,NONE,1.1 MOBYDescriptor.html,NONE,1.1 MOBYPropertyValueException.html,NONE,1.1 MOBYProvider.html,NONE,1.1 MOBYFixedCollection.html,NONE,1.1 MOBYPropertyValue.html,NONE,1.1 MOBYOrderedCollection.html,NONE,1.1 MOBYResizableCollection.html,NONE,1.1 MOBYPropertyValueStatement.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREjs013118@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Added Files: DiscoveryQuery.java URIInvestigator.java MissingPropertyException.java ProviderRemover.java MOBYProperties.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools DiscoveryQuery.java,NONE,1.1 URIInvestigator.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 ProviderRemover.java,NONE,1.1 MOBYProperties.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDJg013033@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph Added Files: MOBYSingleElement.html MOBYSubject.html MOBYResizableCollection.html MOBYPropertyValueException.html MOBYMappingElement.html MOBYOntology.html package-use.html MOBYPropertyValueStatement.html MOBYProviderSet.html MOBYEnumeration.html MOBYGraph.html MOBYObject.html MOBYFixedCollection.html package-tree.html MOBYOrderedCollection.html MOBYResource.html MOBYDocument.html MOBYLiteral.html MOBYUnorderedCollection.html package-summary.html package-frame.html MOBYPropertyValueConstraint.html MOBYProvider.html MOBYPropertyValue.html MOBYGraphNode.html MOBYCollection.html MOBYDescriptor.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph MOBYSingleElement.html,NONE,1.1 MOBYSubject.html,NONE,1.1 MOBYResizableCollection.html,NONE,1.1 MOBYPropertyValueException.html,NONE,1.1 MOBYMappingElement.html,NONE,1.1 MOBYOntology.html,NONE,1.1 package-use.html,NONE,1.1 MOBYPropertyValueStatement.html,NONE,1.1 MOBYProviderSet.html,NONE,1.1 MOBYEnumeration.html,NONE,1.1 MOBYGraph.html,NONE,1.1 MOBYObject.html,NONE,1.1 MOBYFixedCollection.html,NONE,1.1 package-tree.html,NONE,1.1 MOBYOrderedCollection.html,NONE,1.1 MOBYResource.html,NONE,1.1 MOBYDocument.html,NONE,1.1 MOBYLiteral.html,NONE,1.1 MOBYUnorderedCollection.html,NONE,1.1 package-summary.html,NONE,1.1 package-frame.html,NONE,1.1 MOBYPropertyValueConstraint.html,NONE,1.1 MOBYProvider.html,NONE,1.1 MOBYPropertyValue.html,NONE,1.1 MOBYGraphNode.html,NONE,1.1 MOBYCollection.html,NONE,1.1 MOBYDescriptor.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRH9l013432@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Added Files: Test.html ParserTest.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test/class-use Test.html,NONE,1.1 ParserTest.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRDUa013082@pub.open-bio.org> gss Thu Jul 15 16:27:13 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl Added Files: MOBYObjectFactory.html package-use.html package-summary.html MOBYNonNegativeIntegerConstraintImpl.html MOBYDescriptorImpl.html package-frame.html MOBYNonPositiveIntegerConstraintImpl.html package-tree.html MOBYProviderImpl.html MOBYProviderSetImpl.html MOBYDocumentImpl.html MOBYMappingElementImpl.html MOBYDateConstraintImpl.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/graph/impl MOBYObjectFactory.html,NONE,1.1 package-use.html,NONE,1.1 package-summary.html,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.html,NONE,1.1 MOBYDescriptorImpl.html,NONE,1.1 package-frame.html,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.html,NONE,1.1 package-tree.html,NONE,1.1 MOBYProviderImpl.html,NONE,1.1 MOBYProviderSetImpl.html,NONE,1.1 MOBYDocumentImpl.html,NONE,1.1 MOBYMappingElementImpl.html,NONE,1.1 MOBYDateConstraintImpl.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGuP013335@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test Added Files: package-frame.html Test.html package-summary.html ParserTest.html package-tree.html package-use.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/test package-frame.html,NONE,1.1 Test.html,NONE,1.1 package-summary.html,NONE,1.1 ParserTest.html,NONE,1.1 package-tree.html,NONE,1.1 package-use.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREeN013226@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http Added Files: package-summary.html HTTPResponse.html package-frame.html HTTPRequest.html package-tree.html package-use.html HTTPException.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/http package-summary.html,NONE,1.1 HTTPResponse.html,NONE,1.1 package-frame.html,NONE,1.1 HTTPRequest.html,NONE,1.1 package-tree.html,NONE,1.1 package-use.html,NONE,1.1 HTTPException.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFLS013290@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org Added Files: .project .classpath .mymetadata Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org .project,NONE,1.1 .classpath,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREpq013206@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot Added Files: index.html tech-overview.html log4j.properties help1.jpg help.html about.html smoby.example.properties Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot index.html,NONE,1.1 tech-overview.html,NONE,1.1 log4j.properties,NONE,1.1 help1.jpg,NONE,1.1 help.html,NONE,1.1 about.html,NONE,1.1 smoby.example.properties,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIL4013662@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Added Files: greeting greeting.n3 Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies greeting,NONE,1.1 greeting.n3,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGq5013320@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev Added Files: MOBYGraphValidationServlet.java ProviderListServlet.java OWLValidationServlet.java GraphConversionServlet.java RepositoryPrintServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/dev MOBYGraphValidationServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 OWLValidationServlet.java,NONE,1.1 GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGE8013380@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Added Files: HelloWorldServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGAs013410@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies Added Files: index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/ontologies index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHe2013507@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Added Files: Util.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools/class-use Util.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRG0r013350@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet Added Files: package-frame.html AbstractMobyServlet.html ParameterException.html package-summary.html package-use.html ParamReader.html package-tree.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet package-frame.html,NONE,1.1 AbstractMobyServlet.html,NONE,1.1 ParameterException.html,NONE,1.1 package-summary.html,NONE,1.1 package-use.html,NONE,1.1 ParamReader.html,NONE,1.1 package-tree.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHPx013583@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Added Files: DiscoveryServlet.java KeywordSearchServlet.java BaseServlet.java ProviderInvestigationServlet.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets DiscoveryServlet.java,NONE,1.1 KeywordSearchServlet.java,NONE,1.1 BaseServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIvF013645@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save Added Files: index.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save index.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIBQ013599@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources Added Files: inherit.gif Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/resources inherit.gif,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRFrh013275@pub.open-bio.org> gss Thu Jul 15 16:27:15 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter Added Files: index.html top-frame.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter index.html,NONE,1.1 top-frame.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHva013453@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser Added Files: package-use.html package-frame.html UnparsableGraphException.html Parser.html package-summary.html NonCanonicalException.html package-tree.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser package-use.html,NONE,1.1 package-frame.html,NONE,1.1 UnparsableGraphException.html,NONE,1.1 Parser.html,NONE,1.1 package-summary.html,NONE,1.1 NonCanonicalException.html,NONE,1.1 package-tree.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHEI013492@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use Added Files: MOBY.html VocabularyDescription.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/vocabulary/class-use MOBY.html,NONE,1.1 VocabularyDescription.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRGsb013395@pub.open-bio.org> gss Thu Jul 15 16:27:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use Added Files: ParameterException.html AbstractMobyServlet.html ParamReader.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/servlet/class-use ParameterException.html,NONE,1.1 AbstractMobyServlet.html,NONE,1.1 ParamReader.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHCQ013531@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use Added Files: NonCanonicalException.html UnparsableGraphException.html Parser.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/parser/class-use NonCanonicalException.html,NONE,1.1 UnparsableGraphException.html,NONE,1.1 Parser.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRH73013550@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools Added Files: client.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/save/tools client.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRHV7013568@pub.open-bio.org> gss Thu Jul 15 16:27:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Added Files: StorageException.java StorageManager.java Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageException.java,NONE,1.1 StorageManager.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKRIKS013624@pub.open-bio.org> gss Thu Jul 15 16:27:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/.settings Added Files: org.eclipse.core.resources.prefs Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/.settings org.eclipse.core.resources.prefs,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:27:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152027.i6FKREX1013243@pub.open-bio.org> gss Thu Jul 15 16:27:14 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv13012/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools Added Files: package-summary.html Util.html package-tree.html package-frame.html package-use.html Log Message: The real semanticmoby.org source moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/java-api/org/smoby/tools package-summary.html,NONE,1.1 Util.html,NONE,1.1 package-tree.html,NONE,1.1 package-frame.html,NONE,1.1 package-use.html,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:28:53 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:28:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152028.i6FKSrug013743@pub.open-bio.org> gss Thu Jul 15 16:28:53 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv13718/S-MOBY/ref-impl/core/src/org/smoby/parser Modified Files: Parser.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/06/18 21:38:27 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/15 20:28:53 1.5 @@ -6,6 +6,7 @@ import org.smoby.graph.*; import org.smoby.graph.impl.*; import org.smoby.parser.*; +import org.smoby.tools.ModelRetriever; import org.smoby.tools.Util; import org.smoby.vocabulary.*; import com.hp.hpl.jena.rdf.model.*; @@ -28,17 +29,12 @@ public final static String LANGUAGE_N3 = "N3"; /** - * Inference models containing inferred statements derived using - * rdfs:subClassOf relationships. + * Since models are stored in a single Jena model, we + * segregate the single model into multiple sub-models, + * each containing an rdf:type moby:Provider statement, + * plus all statements that are reachable from it. */ - private Map inferenceModels = new HashMap(); - - /** - * Return the inference model associated with a given plain model - */ - private InfModel getInferenceModel(Model model) { - return (InfModel) inferenceModels.get(model); - } + private List subModels = new ArrayList(); /** * Create and return a parser for parsing an N3 file @@ -136,8 +132,7 @@ subModel.setNsPrefixes(model.getNsPrefixMap()); Resource subject = stmt.getSubject(); Util.addReachableStmts(model, subModel, subject, subject.getURI()); - inferenceModels.put(subModel, - ModelFactory.createRDFSModel(subModel)); + subModels.add(subModel); } } @@ -168,7 +163,7 @@ // Parse each provider // - Iterator it = inferenceModels.keySet().iterator(); + Iterator it = subModels.iterator(); while (it.hasNext()) { Model model = (Model) it.next(); @@ -374,13 +369,17 @@ /** * Return a list of statements for whom the subject is a given resource, - * whose predicates is a subproperty of moby:Property, and whose object + * whose predicate is a subproperty of moby:Property, and whose object * is a blank node. */ private List mobyPropertyStatementsOf(Resource res) { + // The statements to return + // List stmts = new ArrayList(); + // Iterate over the statements whose subjects are the resource + // StmtIterator it = res.listProperties(); while (it.hasNext()) { @@ -388,17 +387,16 @@ Property p = stmt.getPredicate(); RDFNode pval = stmt.getObject(); - Model model = res.getModel(); - Model inferenceModel = getInferenceModel(model); + // Try to retrieve a description of the property at + // its URI. + // + InfModel model = getPropertyModel(p); - if (model.contains(res, p, pval) && - inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property)) + if (isMobyProperty(p, model)) { MOBYPropertyValueStatement pvalStmt = MOBYObjectFactory.newPropertyValueStatement(stmt, model); - // See if the property - // Statement s = p.getProperty(RDFS.range); if ((s != null) && (s.getObject().canAs(Resource.class))) @@ -423,6 +421,33 @@ return stmts; } + /** + * Get the model describing a given property by doing a GET + * on its URI, and creating an inference model from it. + */ + private InfModel getPropertyModel(Property p) + { + Model model = ModelRetriever.retrieveModel(p.getURI()); + + if (model == null) { + return null; + } else { + return ModelFactory.createRDFSModel(model); + } + } + + /** + * Return whether or not the given property is a MOBY property. + * This will be true if there is a statement in the model saying + * that the property is an rdfs:subPropertyOf moby:Property. + */ + private boolean isMobyProperty(Property p, InfModel model) + { + return + model != null && + model.contains(p, RDFS.subPropertyOf, MOBY.Property); + } + private String getDataPropertyValue(Resource subject, Property property) { Statement s = subject.getModel().getProperty(subject, property); From gss at pub.open-bio.org Thu Jul 15 20:30:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUG2E013793@pub.open-bio.org> gss Thu Jul 15 16:30:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings In directory pub.open-bio.org:/tmp/cvs-serv13769/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 20:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIeY013882@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Added Files: citation-search.n3 citation-search.rdf Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citation-search.n3,NONE,1.1 citation-search.rdf,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIrT013846@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/05/27 15:31:31 1.10 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/15 20:30:18 1.11 @@ -19,7 +19,7 @@ /** * The provider description graph is stored in a file named "citationSearch" */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; + private final static String DESCRIPTION_GRAPH_FILE = "citation-search.rdf"; /** * Read the description graph from a file named "terms" in the From gss at pub.open-bio.org Thu Jul 15 20:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIjd013866@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF Modified Files: web.xml Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF web.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml 2004/06/10 23:13:44 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml 2004/07/15 20:30:18 1.3 @@ -13,7 +13,7 @@ CitationSearchServlet - /citationSearch + /citation-search From gss at pub.open-bio.org Thu Jul 15 20:30:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:30:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152030.i6FKUIU5013827@pub.open-bio.org> gss Thu Jul 15 16:30:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings In directory pub.open-bio.org:/tmp/cvs-serv13806/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings Added Files: org.eclipse.core.resources.prefs Log Message: Minor fixes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.settings org.eclipse.core.resources.prefs,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:31:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:31:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152031.i6FKV7bk013923@pub.open-bio.org> gss Thu Jul 15 16:31:07 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage In directory pub.open-bio.org:/tmp/cvs-serv13902/S-MOBY/ref-impl/queries/engage Added Files: engage-acmepubs-citation-search.rdf engage-acmepubs-citation-search.n3 Log Message: New queries moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citation-search.rdf,NONE,1.1 engage-acmepubs-citation-search.n3,NONE,1.1 From gss at pub.open-bio.org Thu Jul 15 20:28:04 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:28:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152028.i6FKS4n5013713@pub.open-bio.org> gss Thu Jul 15 16:28:04 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv13688/S-MOBY/ref-impl/core/src/org/smoby/vocabulary Modified Files: MOBY.java Log Message: Changed s-moby.org:8080 to semanticmoby.org moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/06/18 21:39:42 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/15 20:28:04 1.5 @@ -10,7 +10,7 @@ public static String getURI() { - return "http://www.s-moby.org:8080/terms/"; + return "http://www.semanticmoby.org/ontologies/core/"; } public static String getNsPrefix() From gss at pub.open-bio.org Thu Jul 15 20:54:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:54:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152054.i6FKsbhr014079@pub.open-bio.org> gss Thu Jul 15 16:54:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14054/S-MOBY/ref-impl/server/WebRoot Modified Files: domains.html Log Message: Minor fixes moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/06/17 17:35:52 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 20:54:37 1.5 @@ -55,7 +55,7 @@ www.acmepubs.com/citationSearch + "http://www.acmepubs.com:8080/citation-search">www.acmepubs.com/citation-search Provider description graph for acmepubs.com. Note that doing an HTTP GET on this URI @@ -83,11 +83,11 @@ www.megapubs.com/citationSearch + "http://www.megapubs.com:8080/citation-search">www.megapubs.com/citation-search Provider description graph for megapubs.com. The notes regarding the - www.acmepubs.com/citationSearch also apply to this URI.
+ www.acmepubs.com/citation-search also apply to this URI.
From gss at pub.open-bio.org Thu Jul 15 20:58:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 16:58:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152058.i6FKwINQ014126@pub.open-bio.org> gss Thu Jul 15 16:58:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14089/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 citation-search.n3 citation-search.rdf Log Message: Changed to be ASCII moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.7,1.8 citationSearch.n3,1.6,1.7 citation-search.n3,1.1,1.2 citation-search.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/06/16 18:50:59 1.7 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/07/15 20:58:18 1.8 @@ -1,37 +1,37 @@ - - - - - - - - - - - - - - - - - - AcmePubs Citation Search - Industry standard search - - - - - - - - - \ No newline at end of file + + + + + + + + + + + + + + + + + + AcmePubs Citation Search + Industry standard search + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/06/16 18:50:59 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/07/15 20:58:18 1.7 @@ -1,28 +1,28 @@ - at prefix acmepubs: . - at prefix acmeterms: . - at prefix pubs: . - at prefix go: . - at prefix sgd: . - at prefix moby: . - at prefix rdfs: . - at prefix rdf: . - at prefix owl: . - -acmepubs:citationSearch - a moby:Provider, pubs:citationSearch ; - moby:name "AcmePubs Citation Search" ; - moby:oneLineDescription "Industry standard search" ; - moby:operatesOn [ - a rdf:Bag ; - rdf:_1 [ - a moby:Graph ; - moby:hasMapping [ - a moby:Subject, go:GeneSymbol ; - acmeterms:geneSymbol _:bnode1 ; - moby:mapsTo [ - a moby:Object, sgd:LiteratureGuide ; - acmeterms:literatureGuideURI _:bnode2 - ] - ] - ] - ] . \ No newline at end of file + at prefix acmepubs: . + at prefix acmeterms: . + at prefix pubs: . + at prefix go: . + at prefix sgd: . + at prefix moby: . + at prefix rdfs: . + at prefix rdf: . + at prefix owl: . + +acmepubs:citationSearch + a moby:Provider, pubs:citationSearch ; + moby:name "AcmePubs Citation Search" ; + moby:oneLineDescription "Industry standard search" ; + moby:operatesOn [ + a rdf:Bag ; + rdf:_1 [ + a moby:Graph ; + moby:hasMapping [ + a moby:Subject, go:GeneSymbol ; + acmeterms:geneSymbol _:bnode1 ; + moby:mapsTo [ + a moby:Object, sgd:LiteratureGuide ; + acmeterms:literatureGuideURI _:bnode2 + ] + ] + ] + ] . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3 2004/07/15 20:30:18 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.n3 2004/07/15 20:58:18 1.2 @@ -1,28 +1,28 @@ - at prefix acmepubs: . - at prefix acmeterms: . - at prefix pubs: . - at prefix go: . - at prefix sgd: . - at prefix moby: . - at prefix rdfs: . - at prefix rdf: . - at prefix owl: . - -acmepubs:citation-search - a moby:Provider, pubs:citationSearch ; - moby:name "AcmePubs Citation Search" ; - moby:oneLineDescription "Industry standard search" ; - moby:operatesOn [ - a rdf:Bag ; - rdf:_1 [ - a moby:Graph ; - moby:hasMapping [ - a moby:Subject, go:GeneSymbol ; - acmeterms:geneSymbol _:bnode1 ; - moby:mapsTo [ - a moby:Object, sgd:LiteratureGuide ; - acmeterms:literatureGuideURI _:bnode2 - ] - ] - ] + at prefix acmepubs: . + at prefix acmeterms: . + at prefix pubs: . + at prefix go: . + at prefix sgd: . + at prefix moby: . + at prefix rdfs: . + at prefix rdf: . + at prefix owl: . + +acmepubs:citation-search + a moby:Provider, pubs:citationSearch ; + moby:name "AcmePubs Citation Search" ; + moby:oneLineDescription "Industry standard search" ; + moby:operatesOn [ + a rdf:Bag ; + rdf:_1 [ + a moby:Graph ; + moby:hasMapping [ + a moby:Subject, go:GeneSymbol ; + acmeterms:geneSymbol _:bnode1 ; + moby:mapsTo [ + a moby:Object, sgd:LiteratureGuide ; + acmeterms:literatureGuideURI _:bnode2 + ] + ] + ] ] . \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf 2004/07/15 20:30:18 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citation-search.rdf 2004/07/15 20:58:18 1.2 @@ -1,37 +1,37 @@ - - - - - - - - - - - - - Industry standard search - - AcmePubs Citation Search - - - - - - - - - - - - + + + + + + + + + + + + + Industry standard search + + AcmePubs Citation Search + + + + + + + + + + + + \ No newline at end of file From gss at pub.open-bio.org Thu Jul 15 21:01:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:01:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1II3014182@pub.open-bio.org> gss Thu Jul 15 17:01:18 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14159/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot Removed Files: citationSearch.rdf citationSearch.n3 Log Message: Changed name to citation-search moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.8,NONE citationSearch.n3,1.7,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/citationSearch.rdf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/citationSearch.n3,v: No such file or directory From gss at pub.open-bio.org Thu Jul 15 21:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:01:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1gtu014225@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms Modified Files: literatureGuideURI.n3 literatureGuideURI geneSymbol geneSymbol.n3 Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms literatureGuideURI.n3,1.1,1.2 literatureGuideURI,1.1,1.2 geneSymbol,1.1,1.2 geneSymbol.n3,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain sgd:LiteratureGuide ; - rdfs:range xsd:anyURI . \ No newline at end of file + rdfs:range xsd:anyURI . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/literatureGuideURI 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - \ No newline at end of file + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3 2004/06/16 18:50:59 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/geneSymbol.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain go:GeneSymbol ; - rdfs:range xsd:string . \ No newline at end of file + rdfs:range xsd:string . From gss at pub.open-bio.org Thu Jul 15 21:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:01:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1gjA014257@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms Modified Files: literatureGuideURI.n3 geneSymbol geneSymbol.n3 literatureGuideURI Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms literatureGuideURI.n3,1.1,1.2 geneSymbol,1.1,1.2 geneSymbol.n3,1.1,1.2 literatureGuideURI,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain sgd:LiteratureGuide ; - rdfs:range xsd:anyURI . \ No newline at end of file + rdfs:range xsd:anyURI . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - \ No newline at end of file + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/geneSymbol.n3 2004/07/15 21:01:42 1.2 @@ -2,7 +2,7 @@ @prefix xsd: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix owl: . @@ -10,4 +10,4 @@ a owl:DataTypeProperty ; rdfs:subPropertyOf moby:Property ; rdfs:domain go:GeneSymbol ; - rdfs:range xsd:string . \ No newline at end of file + rdfs:range xsd:string . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI 2004/06/16 18:51:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/literatureGuideURI 2004/07/15 21:01:42 1.2 @@ -5,12 +5,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + From gss at pub.open-bio.org Thu Jul 15 21:01:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:01:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152101.i6FL1goc014280@pub.open-bio.org> gss Thu Jul 15 17:01:42 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14188/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Changed URI of moby: to www.semanticmoby.org moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.6,1.7 citationSearch.rdf,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/06/16 18:51:13 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/07/15 21:01:42 1.7 @@ -3,7 +3,7 @@ @prefix pubs: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix rdf: . @prefix owl: . @@ -25,4 +25,4 @@ ] ] ] - ] . \ No newline at end of file + ] . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/06/16 18:51:13 1.7 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/07/15 21:01:42 1.8 @@ -6,16 +6,16 @@ xmlns:go="http://www.go.org:8080/terms/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:moby="http://www.s-moby.org:8080/terms/" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:megaterms="http://www.megapubs.com:8080/terms/" > - + - + Cool new search @@ -27,11 +27,11 @@ - + - + From gss at pub.open-bio.org Thu Jul 15 21:02:11 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:02:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2BQ7014323@pub.open-bio.org> gss Thu Jul 15 17:02:11 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv14298/S-MOBY/ref-impl/server/WebRoot Modified Files: domains.html Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 20:54:37 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/07/15 21:02:11 1.6 @@ -83,7 +83,7 @@ www.megapubs.com/citation-search + "http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch Provider description graph for megapubs.com. The notes regarding the From gss at pub.open-bio.org Thu Jul 15 21:02:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:02:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2dPj014357@pub.open-bio.org> gss Thu Jul 15 17:02:39 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage In directory pub.open-bio.org:/tmp/cvs-serv14328/S-MOBY/ref-impl/queries/engage Modified Files: engage-acmepubs-citationSearch.rdf engage-acmepubs-citationSearch.n3 Log Message: Minor changes moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.rdf,1.2,1.3 engage-acmepubs-citationSearch.n3,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf 2004/06/10 23:27:41 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf 2004/07/15 21:02:39 1.3 @@ -6,35 +6,35 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:pubs="http://www.pubs.org:8081/terms#" - xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" xmlns:sgd="http://www.sgd.org:8080/terms#" > - + - + REV7 - + - + - + - + @@ -48,18 +48,18 @@ Industry standard search http://www.acmepubs.com/about/citationSearch - + AcmePubs Citation Search REV5 - + - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3 2004/06/10 23:27:12 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3 2004/07/15 21:02:39 1.3 @@ -3,7 +3,7 @@ @prefix acmepubs: . @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdfs: . @prefix rdf: . @prefix owl: . From gss at pub.open-bio.org Thu Jul 15 21:02:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 15 Jul 2004 17:02:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407152102.i6FL2doH014380@pub.open-bio.org> gss Thu Jul 15 17:02:39 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery In directory pub.open-bio.org:/tmp/cvs-serv14328/S-MOBY/ref-impl/queries/discovery Modified Files: query.rdf query.n3 Log Message: Minor changes moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.3,1.4 query.n3,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf 2004/06/18 21:45:07 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf 2004/07/15 21:02:39 1.4 @@ -2,17 +2,17 @@ xmlns:sgd="http://www.sgd.org:8080/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:go="http://www.go.org:8080/terms/" - xmlns:moby="http://www.s-moby.org:8080/terms/" > + xmlns:moby="http://www.semanticmoby.org/ontologies/core/" > - + - + - + @@ -22,6 +22,6 @@ - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3 2004/06/18 21:45:07 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3 2004/07/15 21:02:39 1.4 @@ -1,6 +1,6 @@ @prefix go: . @prefix sgd: . - at prefix moby: . + at prefix moby: . @prefix rdf: . _:provider From gss at pub.open-bio.org Mon Jul 19 18:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 19 Jul 2004 14:21:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILat5004196@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/graph Modified Files: MOBYDescriptor.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYDescriptor.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/19 18:21:36 1.2 @@ -2,6 +2,8 @@ import java.net.URI; +import com.hp.hpl.jena.rdf.model.Resource; + /** * The Resource interface represents things that are available * at a URI. @@ -11,5 +13,5 @@ /** * Return the URI represented by this node. */ - public String getURI(); + public Resource getResource(); } From gss at pub.open-bio.org Mon Jul 19 18:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 19 Jul 2004 14:21:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILaer004215@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/parser Modified Files: Parser.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/15 20:28:53 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/19 18:21:36 1.6 @@ -212,8 +212,8 @@ // oneLineDescription, aboutURI, and collection of operatesOn subgraphs // return MOBYObjectFactory.newProvider( - provider.getURI(), name, oneLiner, aboutURI, - MOBYObjectFactory.newUnorderedCollection(null, operatesOn, model), + provider, name, oneLiner, aboutURI, + MOBYObjectFactory.newUnorderedCollection(provider, operatesOn, model), model); } @@ -234,7 +234,7 @@ // hasMapping property that leads to its mapping subgraph. // Resource hasMapping = getResourcePropertyValue(res, MOBY.hasMapping); - return MOBYObjectFactory.newGraph(null, parseHasMapping(hasMapping), model); + return MOBYObjectFactory.newGraph(res, parseHasMapping(hasMapping), model); } else { @@ -318,9 +318,9 @@ // Create and return a Subject to describe this hasMapping subgraph // - return MOBYObjectFactory.newSubject(res.getURI(), - MOBYObjectFactory.newFixedCollection(null, statements, model), - MOBYObjectFactory.newUnorderedCollection(null, directMappings, model), + return MOBYObjectFactory.newSubject(res, + MOBYObjectFactory.newFixedCollection(res, statements, model), + MOBYObjectFactory.newUnorderedCollection(res, directMappings, model), collectionFor(res, nestedMappings), model); } @@ -362,8 +362,8 @@ // Create and return a new MOBYObject // Model model = res.getModel(); - return MOBYObjectFactory.newObject(res.getURI(), - MOBYObjectFactory.newFixedCollection(null, statements, model), + return MOBYObjectFactory.newObject(res, + MOBYObjectFactory.newFixedCollection(res, statements, model), collectionFor(res, nested), model); } @@ -486,13 +486,13 @@ private MOBYCollection collectionFor(Resource res, List elements) { if (isList(res)) { - return MOBYObjectFactory.newFixedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newFixedCollection(res, elements, res.getModel()); } else if (isBag(res)) { - return MOBYObjectFactory.newUnorderedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newUnorderedCollection(res, elements, res.getModel()); } else if (isSeq(res)) { - return MOBYObjectFactory.newOrderedCollection(null, elements, res.getModel()); + return MOBYObjectFactory.newOrderedCollection(res, elements, res.getModel()); } else if (isAlt(res)) { - return MOBYObjectFactory.newEnumeration(null, elements, res.getModel()); + return MOBYObjectFactory.newEnumeration(res, elements, res.getModel()); } else { return null; } From gss at pub.open-bio.org Mon Jul 19 18:21:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 19 Jul 2004 14:21:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407191821.i6JILaxW004177@pub.open-bio.org> gss Mon Jul 19 14:21:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv4088/src/org/smoby/graph/impl Modified Files: MOBYProviderImpl.java MOBYFixedCollectionImpl.java MOBYResizableCollectionImpl.java MOBYObjectImpl.java MOBYUnorderedCollectionImpl.java MOBYDocumentImpl.java MOBYGraphImpl.java MOBYMappingElementImpl.java MOBYOrderedCollectionImpl.java MOBYOntologyImpl.java MOBYEnumerationImpl.java MOBYDescriptorImpl.java MOBYCollectionImpl.java MOBYSubjectImpl.java MOBYGraphNodeImpl.java MOBYSingleElementImpl.java MOBYObjectFactory.java Log Message: Changes to API exposes more of Jena API moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderImpl.java,1.1,1.2 MOBYFixedCollectionImpl.java,1.1,1.2 MOBYResizableCollectionImpl.java,1.1,1.2 MOBYObjectImpl.java,1.1,1.2 MOBYUnorderedCollectionImpl.java,1.1,1.2 MOBYDocumentImpl.java,1.1,1.2 MOBYGraphImpl.java,1.1,1.2 MOBYMappingElementImpl.java,1.1,1.2 MOBYOrderedCollectionImpl.java,1.1,1.2 MOBYOntologyImpl.java,1.1,1.2 MOBYEnumerationImpl.java,1.1,1.2 MOBYDescriptorImpl.java,1.1,1.2 MOBYCollectionImpl.java,1.1,1.2 MOBYSubjectImpl.java,1.1,1.2 MOBYGraphNodeImpl.java,1.1,1.2 MOBYSingleElementImpl.java,1.1,1.2 MOBYObjectFactory.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYProviderImpl.java 2004/07/19 18:21:36 1.2 @@ -16,11 +16,11 @@ private MOBYUnorderedCollection operatesOn; private Model underlying; - MOBYProviderImpl(String uri, String name, String oneLineDescription, + MOBYProviderImpl(Resource resource, String name, String oneLineDescription, String moreInfoURI, MOBYUnorderedCollection operatesOn, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.name = name; this.oneLineDescription = oneLineDescription; this.moreInfoURI = moreInfoURI; =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYFixedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,16 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYFixedCollectionImpl extends MOBYCollectionImpl implements MOBYFixedCollection { - public MOBYFixedCollectionImpl(String uri, List elements, Model underlying) + public MOBYFixedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isResizable() { return false; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYResizableCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,16 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; abstract class MOBYResizableCollectionImpl extends MOBYCollectionImpl implements MOBYResizableCollection { - MOBYResizableCollectionImpl(String uri, List elements, Model underlying) + MOBYResizableCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isResizable() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectImpl.java 2004/07/19 18:21:36 1.2 @@ -3,14 +3,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYObjectImpl extends MOBYMappingElementImpl implements MOBYObject { - MOBYObjectImpl(String uri, MOBYFixedCollection statements, + MOBYObjectImpl(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedElements, Model underlying) { - super(uri, statements, nestedElements, underlying); + super(resource, statements, nestedElements, underlying); } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYUnorderedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,14 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYUnorderedCollectionImpl extends MOBYResizableCollectionImpl implements MOBYUnorderedCollection { - MOBYUnorderedCollectionImpl(String uri, List elements, Model underlying) + MOBYUnorderedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isOrdered() { return false; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDocumentImpl.java 2004/07/19 18:21:36 1.2 @@ -8,8 +8,8 @@ extends MOBYDescriptorImpl implements MOBYDocument { - MOBYDocumentImpl(String uri, Model underlying) + MOBYDocumentImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYGraphImpl extends MOBYSingleElementImpl @@ -10,9 +11,9 @@ { private MOBYGraphNode hasMapping; - MOBYGraphImpl(String uri, MOBYGraphNode hasMapping, Model underlying) + MOBYGraphImpl(Resource resource, MOBYGraphNode hasMapping, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.hasMapping = hasMapping; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYMappingElementImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; public class MOBYMappingElementImpl extends MOBYSingleElementImpl @@ -11,10 +12,10 @@ private MOBYFixedCollection statements; private MOBYCollection nestedElements; - public MOBYMappingElementImpl(String uri, MOBYFixedCollection statements, + public MOBYMappingElementImpl(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedElements, Model underlying) { - super(uri, underlying); + super(resource, underlying); this.statements = statements; this.nestedElements = nestedElements; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOrderedCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -5,15 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYOrderedCollectionImpl extends MOBYResizableCollectionImpl implements MOBYOrderedCollection { - - public MOBYOrderedCollectionImpl(String uri, List elements, Model underlying) + public MOBYOrderedCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isOrdered() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYOntologyImpl.java 2004/07/19 18:21:36 1.2 @@ -7,7 +7,7 @@ extends MOBYDocumentImpl implements MOBYOntology { - MOBYOntologyImpl(String uri, Model underlying) { - super(uri, underlying); + MOBYOntologyImpl(Resource resource, Model underlying) { + super(resource, underlying); } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYEnumerationImpl.java 2004/07/19 18:21:36 1.2 @@ -10,9 +10,9 @@ extends MOBYUnorderedCollectionImpl implements MOBYEnumeration { - MOBYEnumerationImpl(String uri, List elements, Model underlying) + MOBYEnumerationImpl(Resource resource, List elements, Model underlying) { - super(uri, elements, underlying); + super(resource, elements, underlying); } public boolean isEnumeration() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYDescriptorImpl.java 2004/07/19 18:21:36 1.2 @@ -6,21 +6,26 @@ public abstract class MOBYDescriptorImpl implements MOBYDescriptor { protected Model underlying; - protected String uri; + protected Resource resource; - MOBYDescriptorImpl(String uri, Model underlying) + MOBYDescriptorImpl(Resource resource, Model underlying) { - this.uri = uri; + this.resource = resource; this.underlying = underlying; } - public String getURI() + public Resource getResource() { - return uri; + return resource; } public Model getUnderlying() { return underlying; } + + public String getURI() + { + return (resource == null) ? null : resource.getURI(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYCollectionImpl.java 2004/07/19 18:21:36 1.2 @@ -1,9 +1,7 @@ package org.smoby.graph.impl; import org.smoby.graph.*; - -import com.hp.hpl.jena.rdf.model.Model; - +import com.hp.hpl.jena.rdf.model.*; import java.util.*; abstract class MOBYCollectionImpl @@ -12,9 +10,9 @@ { protected List elements = new ArrayList(); - MOBYCollectionImpl(String uri, List elements, Model underlying) + MOBYCollectionImpl(Resource resource, List elements, Model underlying) { - super(uri, underlying); + super(resource, underlying); for (Iterator it = elements.iterator(); it.hasNext();) { this.elements.add(it.next()); } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSubjectImpl.java 2004/07/19 18:21:36 1.2 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYSubjectImpl extends MOBYMappingElementImpl @@ -10,11 +11,11 @@ { private MOBYUnorderedCollection directMappings; - MOBYSubjectImpl(String uri, MOBYFixedCollection statements, + MOBYSubjectImpl(Resource resource, MOBYFixedCollection statements, MOBYUnorderedCollection directMappings, MOBYCollection nestedMappings, Model underlying) { - super(uri, statements, nestedMappings, underlying); + super(resource, statements, nestedMappings, underlying); this.directMappings = directMappings; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYGraphNodeImpl.java 2004/07/19 18:21:36 1.2 @@ -1,19 +1,18 @@ package org.smoby.graph.impl; import org.smoby.graph.*; - -import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.*; abstract class MOBYGraphNodeImpl extends MOBYDescriptorImpl implements MOBYGraphNode { - MOBYGraphNodeImpl(String uri, Model underlying) + MOBYGraphNodeImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } public boolean isBlank() { - return getURI() == null; + return (resource == null) || (resource.getURI() == null); } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java 2004/05/24 22:05:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYSingleElementImpl.java 2004/07/19 18:21:36 1.2 @@ -5,14 +5,15 @@ import org.smoby.graph.*; import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; class MOBYSingleElementImpl extends MOBYGraphNodeImpl implements MOBYSingleElement { - MOBYSingleElementImpl(String uri, Model underlying) + MOBYSingleElementImpl(Resource resource, Model underlying) { - super(uri, underlying); + super(resource, underlying); } public boolean isSingular() { return true; } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java 2004/06/18 21:37:52 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java 2004/07/19 18:21:36 1.3 @@ -3,6 +3,7 @@ import org.smoby.graph.*; import org.smoby.graph.impl.*; import com.hp.hpl.jena.rdf.model.*; + import java.util.*; /** @@ -11,32 +12,32 @@ */ public final class MOBYObjectFactory { - public static MOBYFixedCollection newFixedCollection(String uri, List elements, Model underlying) + public static MOBYFixedCollection newFixedCollection(Resource resource, List elements, Model underlying) { - return new MOBYFixedCollectionImpl(uri, elements, underlying); + return new MOBYFixedCollectionImpl(resource, elements, underlying); } - public static MOBYOrderedCollection newOrderedCollection(String uri, List elements, Model underlying) + public static MOBYOrderedCollection newOrderedCollection(Resource resource, List elements, Model underlying) { - return new MOBYOrderedCollectionImpl(uri, elements, underlying); + return new MOBYOrderedCollectionImpl(resource, elements, underlying); } - public static MOBYUnorderedCollection newUnorderedCollection(String uri, List elements, Model underlying) + public static MOBYUnorderedCollection newUnorderedCollection(Resource resource, List elements, Model underlying) { - return new MOBYUnorderedCollectionImpl(uri, elements, underlying); + return new MOBYUnorderedCollectionImpl(resource, elements, underlying); } - public static MOBYEnumeration newEnumeration(String uri, List elements, Model underlying) + public static MOBYEnumeration newEnumeration(Resource resource, List elements, Model underlying) { - return new MOBYEnumerationImpl(uri, elements, underlying); + return new MOBYEnumerationImpl(resource, elements, underlying); } public static MOBYProvider newProvider( - String uri, String name, String oneLineDescription, + Resource resource, String name, String oneLineDescription, String moreInfoURI, MOBYUnorderedCollection operatesOn, Model underlying) { - return new MOBYProviderImpl(uri, name, oneLineDescription, moreInfoURI, operatesOn, + return new MOBYProviderImpl(resource, name, oneLineDescription, moreInfoURI, operatesOn, underlying); } @@ -45,24 +46,24 @@ return new MOBYProviderSetImpl(); } - public static MOBYGraph newGraph(String uri, MOBYGraphNode hasMapping, Model underlying) + public static MOBYGraph newGraph(Resource resource, MOBYGraphNode hasMapping, Model underlying) { - return new MOBYGraphImpl(uri, hasMapping, underlying); + return new MOBYGraphImpl(resource, hasMapping, underlying); } public static MOBYSubject newSubject( - String uri, MOBYFixedCollection statements, + Resource resource, MOBYFixedCollection statements, MOBYUnorderedCollection directMappings, MOBYCollection nestedMappings, Model underlying) { - return new MOBYSubjectImpl(uri, statements, directMappings, + return new MOBYSubjectImpl(resource, statements, directMappings, nestedMappings, underlying); } - public static MOBYObject newObject(String uri, MOBYFixedCollection statements, + public static MOBYObject newObject(Resource resource, MOBYFixedCollection statements, MOBYCollection nestedMappings, Model underlying) { - return new MOBYObjectImpl(uri, statements, nestedMappings, underlying); + return new MOBYObjectImpl(resource, statements, nestedMappings, underlying); } public static MOBYPropertyValueStatement newPropertyValueStatement( From gss at pub.open-bio.org Mon Jul 19 21:22:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 19 Jul 2004 17:22:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407192122.i6JLM94E004903@pub.open-bio.org> gss Mon Jul 19 17:22:09 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv4878/src/org/smoby/vocabulary Modified Files: MOBY.java Log Message: Added keyword property moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/15 20:28:04 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/19 21:22:09 1.6 @@ -36,4 +36,5 @@ public static final Property mapsTo = property(getURI(), "mapsTo"); public static final Property lastModifiedDate = property(getURI(), "lastModifiedDate"); public static final Property Property = property(getURI(), "Property"); + public static final Property keyword = property(getURI(), "keyword"); } \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 21:59:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 17:59:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212159.i6LLxocL012810@pub.open-bio.org> gss Wed Jul 21 17:59:50 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv12789/S-MOBY/ref-impl/core/src/org/smoby/graph Added Files: MOBYGraphVisitor.java Log Message: Placeholder moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYGraphVisitor.java,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 22:00:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:00:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212200.i6LM0KnH012853@pub.open-bio.org> gss Wed Jul 21 18:00:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org In directory pub.open-bio.org:/tmp/cvs-serv12828/S-MOBY/ref-impl/semanticmoby.org Modified Files: .mymetadata Log Message: Minor changes moby-live/S-MOBY/ref-impl/semanticmoby.org .mymetadata,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata 2004/07/21 22:00:20 1.2 @@ -1,6 +1,7 @@ - + From gss at pub.open-bio.org Wed Jul 21 22:01:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1GA7012884@pub.open-bio.org> gss Wed Jul 21 18:01:16 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv12860/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Jul 21 22:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JRA012926@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Added Files: cshl-logo.jpg nsf-logo.jpg help1.png ncgr-logo.jpg rdf-logo.PNG Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images cshl-logo.jpg,NONE,1.1 nsf-logo.jpg,NONE,1.1 help1.png,NONE,1.1 ncgr-logo.jpg,NONE,1.1 rdf-logo.PNG,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 22:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JKj012949@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Modified Files: KeywordSearchServlet.java BaseServlet.java Added Files: ProviderEngagementServlet.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets ProviderEngagementServlet.java,NONE,1.1 KeywordSearchServlet.java,1.1,1.2 BaseServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:01:19 1.2 @@ -1,10 +1,11 @@ package org.smoby.ref.servlets; import java.io.*; - +import java.util.*; import javax.servlet.*; import javax.servlet.http.*; -import javax.servlet.http.HttpServletResponse; +import org.smoby.graph.*; +import org.smoby.ref.tools.*; public class KeywordSearchServlet extends BaseServlet { @@ -12,37 +13,121 @@ throws ServletException, IOException { PrintStream out = new PrintStream(response.getOutputStream()); + + List provider = getKeywords("provider", request); + List accepts = getKeywords("accepts", request); + List returns = getKeywords("returns", request); + startHTML(response, out); + if ((provider == null) && (accepts == null) && (returns == null)) + { + showResultCount(-1, out); + } + else + { + KeywordQuery q = new KeywordQuery(provider, accepts, returns); + + List matching = q.findMatchingProviders(); + + showResultCount(matching.size(), out); + + for (Iterator it = matching.iterator(); it.hasNext();) + { + MOBYProvider p = (MOBYProvider) it.next(); + showProvider(p, out); + } + } finishHTML(response, out); } - private void startHTML(HttpServletResponse response, PrintStream out) + private List getKeywords(String paramName, HttpServletRequest request) { - response.setContentType("text/html"); - out.println(""); - out.println(""); - out.println("Semantic MOBY search results"); - out.println(""); - out.println("

"); - out.println("Semantic"); - out.println("M" + - "OBY"); - out.println("

"); + List keywords = new ArrayList(); + + String value = request.getParameter(paramName); + if (value == null) return keywords; + + value = value.trim(); + + if (value.length() == 0) return keywords; + + StreamTokenizer st = new StreamTokenizer(new StringReader(value)); + st.wordChars('*', '*'); + st.wordChars('%', '%'); + try + { + while (st.nextToken() != StreamTokenizer.TT_EOF) + { + if (st.sval != null) + { + String val = st.sval.toLowerCase().trim().replace('*', '%'); + keywords.add(val); + } + } + } catch (IOException e) {} + + return keywords; } private void showResultCount(int count, PrintStream out) { - if (count < 1) { - out.println("No matches"); + out.println(""); + out.println(""); + out.println(""); + out.println(""); + out.println("
"); + + if (count < 0) { + out.println("No keywords were entered, so no search was performed."); + } else if (count < 1) { + out.println("No matching providers were found. Note that"); + out.println("very few providers have yet been defined."); } else { - out.println("" + count + " results found:"); + out.println(count + " matching provider" + + (count > 1 ? "s" : "") + " found"); } + out.println("
"); + out.println("
"); } - private void finishHTML(HttpServletResponse response, PrintStream out) + private void showProvider(MOBYProvider provider, PrintStream out) { - response.setContentType("text/html"); - out.println(""); + String uri = provider.getResource().getURI(); + String name = provider.getName(); + String description = provider.getOneLineDescription(); + String moreInfo = provider.getMoreInfoURI(); + + out.println(""); + out.print(""); + if ((name != null) && (name.trim().length() > 0)) { + out.println(name); + } else { + out.println(uri); + } + out.print(""); + out.println(""); + out.print(""); + out.print("\"Definition\""); + out.print(""); + out.println("
"); + + if ((description != null) && (description.trim().length() > 0)) { + out.println(description); + } else { + out.println("No description is available for this provider."); + } + out.println("
"); + + if ((moreInfo != null) && (moreInfo.trim().length() > 0)) { + out.println("For more information see " + moreInfo + ""); + } + out.println("
"); } public void doPost(HttpServletRequest request, HttpServletResponse response) =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/BaseServlet.java 2004/07/21 22:01:19 1.2 @@ -5,6 +5,7 @@ import javax.servlet.*; import javax.servlet.http.*; + import org.smoby.ref.tools.*; import org.smoby.servlet.*; import org.apache.log4j.*; @@ -48,4 +49,32 @@ } } } + + protected void startHTML(HttpServletResponse response, PrintStream out) + { + response.setContentType("text/html"); + out.println(""); + out.println(""); + out.println("Semantic MOBY search results"); + out.println(""); + out.println("
"); + out.println("

"); + out.println(""); + out.println("Semantic"); + out.println("M" + + "OBY" + + ""); + out.println(""); + out.println("

"); + out.println("
"); + out.println(""); + out.println(""); + } + + protected void finishHTML(HttpServletResponse response, PrintStream out) + { + out.println(""); + out.println(""); + out.println(""); + } } \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 22:01:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1JDv012969@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example Modified Files: HelloWorldServlet.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/15 20:27:16 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/21 22:01:19 1.2 @@ -4,6 +4,7 @@ import java.util.*; import javax.servlet.*; import javax.servlet.http.*; + import org.smoby.graph.*; import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.ref.servlets.*; @@ -48,4 +49,12 @@ // Silently ignore graphs without the required form catch (Throwable t) {} } + + /** + * Return the last modification date of the description graph file + */ + public long getLastModified(HttpServletRequest request) + { + return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); + } } From gss at pub.open-bio.org Wed Jul 21 22:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KvG013015@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot Modified Files: help.html index.html Added Files: .cvsignore Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot .cvsignore,NONE,1.1 help.html,1.1,1.2 index.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:01:20 1.2 @@ -1,26 +1,56 @@ -Semantic MOBY Help +Semantic MOBY Search Help

Semantic MOBY -Help +Search Help

-
-

+ Semantic MOBY maintains a searchable repository of descriptions of -providers of services that are available on the web. At the heart -of these descriptions is the notion of mapping, that a provider -"accepts" one type of thing, maps it to another thing that it returns -as a result. For example, entering -the following terms is asking Semantic MOBY to search its repository -for providers that accept terms described as "gene symbols" and return -things whose descriptions match the wildcard pattern "publication*". +providers of services that are available on the web. At the heart +of these descriptions is the notion that providers map one type +of thing (what the provider accepts) to another type of thing (what +the provider returns). +

+Providers, as well as things accepted and returned by providers, are +classified using web-accessible descriptions, and these descriptions +have keywords associated with them. For example, the following shows +a query for providers whose descriptions include the keyword "hello":

-. +.
+
+Search hints +
    +
  • Keywords are not case sensitive, so HELLO means the +same thing as hello as does HeLloW. +

    +
  • The wildcard character (*) can be used at the end of a keyword +to match keywords that start with the characters before the wildcard. +For example, he* will match hello as well +as help. +

    +
  • Multiple words enclosed in double quotes are considered to be a +single keyword. For example, the quoted string "gene symbol" +is considered to be a single keyword composed of 11 characters, including a space. +The wildcard character is interpreted literally (i.e. as the '*' +character) if it appears within a quoted string. +

    +
  • Multiple keywords may be typed in one of the fields; this means to +search for any of the keywords in that field. For example, +typing fat sugar in the accepts field will search for +providers that map either fat or sugar to something else. +

    +
  • If keywords are typed in multiple fields, then only providers that +match keywords for all the fields will match. For example, +typing fat sugar into the accepts field, and +"weight gain" into the returns field will search for +providers that map either fat or sugar to weight gain. +

    +
=================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:01:20 1.2 @@ -16,21 +16,45 @@ Accepts Returns - - - + + +
Type any terms into the boxes above and press Search
-(for example type Hello into the Provider box) +(for example type 'hello' (without quotes) into the Provider box)

-

About Semantic MOBY   Help on Searching +


+ + + + + + + + + + + +
+ + CSHL + + NCGR + + NSF
+ + Cold Spring Harbor Laboratory + + National Center for Genome Resources + + National Science Foundation
From gss at pub.open-bio.org Wed Jul 21 22:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KM9013059@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello Modified Files: hello-world.n3 hello-world.rdf Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello hello-world.n3,1.1,1.2 hello-world.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.n3 2004/07/21 22:01:20 1.2 @@ -7,7 +7,7 @@ @prefix xsd: . ex:hello-world - a moby:Provider ; + a moby:Provider, exterms:GreetingProvider ; moby:name "Semantic MOBY Hello World provider" ; moby:oneLineDescription "Simple example of a Semantic MOBY provider" ; moby:operatesOn [ =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf 2004/07/15 20:27:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/hello/hello-world.rdf 2004/07/21 22:01:20 1.2 @@ -8,20 +8,21 @@ xmlns:moby="http://www.semanticmoby.org/ontologies/core/" > + Simple example of a Semantic MOBY provider Semantic MOBY Hello World provider - - - - - + - + + + + + \ No newline at end of file From gss at pub.open-bio.org Wed Jul 21 22:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1Kfw012988@pub.open-bio.org> gss Wed Jul 21 18:01:19 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools Modified Files: URIInvestigator.java Added Files: KeywordQuery.java KeywordList.java KeywordFinder.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools KeywordQuery.java,NONE,1.1 KeywordList.java,NONE,1.1 KeywordFinder.java,NONE,1.1 URIInvestigator.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java 2004/07/15 20:27:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/URIInvestigator.java 2004/07/21 22:01:19 1.2 @@ -216,7 +216,8 @@ // retrievable, but register the graph anyway // syncLog.warn("Unable to get Last-Modified date for " - + providerURI + "; ignoring"); + + providerURI + "; using current date"); + lastModifiedDate = new Date(); } catch (Throwable t) { From gss at pub.open-bio.org Wed Jul 21 22:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1Knv013083@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageManager.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/15 20:27:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/21 22:01:20 1.2 @@ -9,6 +9,8 @@ import com.hp.hpl.jena.rdf.model.*; import com.hp.hpl.jena.shared.*; import com.hp.hpl.jena.vocabulary.*; +import java.sql.Connection; +import java.sql.SQLException; import java.util.*; /** @@ -60,7 +62,7 @@ { Model model = ((MOBYProviderImpl) provider).getUnderlying(); Model dbModel = null; - String uriString = provider.getURI(); + String uriString = provider.getResource().getURI(); Resource uri = model.createResource(uriString); try @@ -100,6 +102,12 @@ dbModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime()); } + // Add keywords associated with the provider + // + KeywordFinder finder = new KeywordFinder(provider, model); + addKeywords(provider.getResource().getURI(), + finder.getKeywords(), dbModel); + // Commit the transaction on the database model // dbModel.commit(); @@ -116,6 +124,73 @@ } } } + + private void addKeywords(String providerURI, KeywordList list, Model model) + throws StorageException + { + try + { + ModelRDB dbModel = (ModelRDB) model; + Connection conn = dbModel.getConnection().getConnection(); + + java.sql.Statement sql = conn.createStatement(); + + doAddKeywords(providerURI, list.getProviderKeywords(), "P", sql); + doAddKeywords(providerURI, list.getSubjectKeywords(), "S", sql); + doAddKeywords(providerURI, list.getObjectKeywords(), "O", sql); + + } + catch (Throwable t) + { + throw new StorageException(t); + } + } + + private void doAddKeywords(String providerURI, Iterator it, + String appliesTo, java.sql.Statement sql) + throws SQLException + { + while (it.hasNext()) + { + String keyword = it.next().toString(); + + StringBuffer sb = new StringBuffer(); + + sb.append("INSERT INTO MOBY_KEYWORD\n"); + sb.append(" (keyword, provider_uri, applies_to)\n"); + sb.append("values ('"); + sb.append(keyword.toLowerCase().trim()); + sb.append("', '"); + sb.append(providerURI); + sb.append("', '"); + sb.append(appliesTo); + sb.append("')"); + + String queryString = sb.toString(); + + sql.execute(queryString); + } + } + + private void removeKeywords(String providerURI, Model model) + throws StorageException + { + try + { + ModelRDB dbModel = (ModelRDB) model; + Connection conn = dbModel.getConnection().getConnection(); + + java.sql.Statement sql = conn.createStatement(); + + sql.execute("DELETE FROM MOBY_KEYWORD WHERE provider_uri = '" + + providerURI + "'"); + + } + catch (Throwable t) + { + throw new StorageException(t); + } + } /** * Remove all the statements registered by a given provider URI @@ -143,6 +218,10 @@ // ProviderRemover.remove(dbModel, providerURI); + // Remove keywords associated with the provider URI + // + removeKeywords(providerURI, dbModel); + // Commit the transaction on the database // dbModel.commit(); From gss at pub.open-bio.org Wed Jul 21 22:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KH3013030@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies Added Files: GreetingProvider.n3 GreetingProvider index.html Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/ontologies GreetingProvider.n3,NONE,1.1 GreetingProvider,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Wed Jul 21 22:01:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:01:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212201.i6LM1KKL013102@pub.open-bio.org> gss Wed Jul 21 18:01:20 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF Modified Files: web.xml Log Message: Many changes prior to BOSC moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/WEB-INF/web.xml 2004/07/21 22:01:20 1.2 @@ -17,6 +17,13 @@ + ProviderEngagementServlet + engage-provider + Keyword search servlet + org.smoby.ref.servlets.ProviderEngagementServlet + + + HelloWorldServlet hello-world Hello World simple application @@ -64,6 +71,11 @@ + ProviderEngagementServlet + /engage-provider + + + HelloWorldServlet /examples/hello-world From gss at pub.open-bio.org Wed Jul 21 22:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:35:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZP58013212@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images Modified Files: help1.png Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images help1.png,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png 2004/07/21 22:01:19 1.1 and /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png 2004/07/21 22:35:25 1.2 differ rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/help1.png: diff failed From gss at pub.open-bio.org Wed Jul 21 22:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:35:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZP6f013240@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/WebRoot Modified Files: help.html tech-overview.html index.html Removed Files: help1.jpg Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot help.html,1.2,1.3 tech-overview.html,1.1,1.2 index.html,1.2,1.3 help1.jpg,1.1,NONE =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2004/07/21 22:35:25 1.3 @@ -13,13 +13,13 @@ Semantic MOBY maintains a searchable repository of descriptions of providers of services that are available on the web. At the heart of these descriptions is the notion that providers map one type -of thing (what the provider accepts) to another type of thing (what -the provider returns). +of thing (the Subject) to another (the Object), or +vice versa.

-Providers, as well as things accepted and returned by providers, are -classified using web-accessible descriptions, and these descriptions +Providers, as well as subjects and objects, are +classified using web-accessible definitions (ontologies), and these definitions have keywords associated with them. For example, the following shows -a query for providers whose descriptions include the keyword "hello": +a query for providers whose definitions include the keyword "hello":

. @@ -28,7 +28,7 @@ Search hints
  • Keywords are not case sensitive, so HELLO means the -same thing as hello as does HeLloW. +same thing as hello as does HeLlO.

  • The wildcard character (*) can be used at the end of a keyword to match keywords that start with the characters before the wildcard. @@ -43,13 +43,13 @@

  • Multiple keywords may be typed in one of the fields; this means to search for any of the keywords in that field. For example, -typing fat sugar in the accepts field will search for +typing fat sugar in the Subject field will search for providers that map either fat or sugar to something else.

  • If keywords are typed in multiple fields, then only providers that match keywords for all the fields will match. For example, -typing fat sugar into the accepts field, and -"weight gain" into the returns field will search for +typing fat sugar into the Subject field, and +"weight gain" into the Object field will search for providers that map either fat or sugar to weight gain.

=================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html 2004/07/15 20:27:14 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/tech-overview.html 2004/07/21 22:35:25 1.2 @@ -34,7 +34,11 @@ a Semantic MOBY provider, and should be examined first. -Graph
converter + + +Graph
converter + + An example that converts among various formats of OWL graphs. =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:35:25 1.3 @@ -13,8 +13,8 @@ - - + + @@ -45,15 +45,20 @@ NSF + CSHL + NCGR + NSF + + +
ProviderAcceptsReturns
SubjectObject
- - Cold Spring Harbor Laboratory - - National Center for Genome Resources - - National Science Foundation
+
+
+ +
+Under Construction - Pardon the Dust
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/RCS/help1.jpg,v: No such file or directory From gss at pub.open-bio.org Wed Jul 21 22:35:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 21 Jul 2004 18:35:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407212235.i6LMZPGs013260@pub.open-bio.org> gss Wed Jul 21 18:35:25 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv13187/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets Modified Files: KeywordSearchServlet.java Log Message: Last-minute changes moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets KeywordSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:01:19 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/KeywordSearchServlet.java 2004/07/21 22:35:25 1.3 @@ -19,7 +19,7 @@ List returns = getKeywords("returns", request); startHTML(response, out); - if ((provider == null) && (accepts == null) && (returns == null)) + if ((provider.isEmpty()) && (accepts.isEmpty()) && (returns.isEmpty())) { showResultCount(-1, out); } From mwilkinson at pub.open-bio.org Mon Jul 26 17:09:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 26 Jul 2004 13:09:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407261709.i6QH99FA005183@pub.open-bio.org> mwilkinson Mon Jul 26 13:09:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv5164/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: fixed a nasty bug that was preventing the proper registration of collection output services moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/09 00:21:53 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/26 17:09:09 1.3 @@ -102,23 +102,23 @@ sub insert_collection_input { my ($self, %args) = @_; my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ +# if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ # this should be dropped down into the mysql.pm module?? probably... $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); my $id=$self->dbh->{mysql_insertid}; return $id; - } +# } } sub insert_collection_output { my ($self, %args) = @_; my $dbh = $self->dbh; - if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ +# if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){ # this should be dropped down into the mysql.pm module?? probably... $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name})); my $id=$self->dbh->{mysql_insertid}; return $id; - } +# } } sub insert_simple_input { From mwilkinson at pub.open-bio.org Tue Jul 27 22:56:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 27 Jul 2004 18:56:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407272256.i6RMuXo3012522@pub.open-bio.org> mwilkinson Tue Jul 27 18:56:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv12503/MOBY/Client Modified Files: CollectionArticle.pm Log Message: simples were being added to collections multiple times when creating a ServiceInstance from a DOM, rather than from parsing the XML manually. Fixed. RDF should now be somewhat more sensible. moby-live/Perl/MOBY/Client CollectionArticle.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/06/15 00:37:55 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2004/07/27 22:56:32 1.9 @@ -306,10 +306,7 @@ $self->articleName($articleName); my $objects = $dom->getElementsByTagName("Simple"); for my $n(0..$objects->getLength - 1){ - foreach my $child($objects->item($n)->getChildNodes){ - next unless $child->getNodeType == ELEMENT_NODE; - $self->addSimple(MOBY::Client::SimpleArticle->new(articleName=>$self->articleName, XML_DOM => $objects->item($n))); - } + $self->addSimple(MOBY::Client::SimpleArticle->new(articleName=>$self->articleName, XML_DOM => $objects->item($n))); } return $self; } From mwilkinson at pub.open-bio.org Wed Jul 28 22:55:14 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 18:55:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282255.i6SMtEH9016063@pub.open-bio.org> mwilkinson Wed Jul 28 18:55:13 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16045/RDF Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/RDF added to the repository moby-live/Perl/MOBY/RDF - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Wed Jul 28 22:56:59 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 18:56:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282256.i6SMuxUG016129@pub.open-bio.org> mwilkinson Wed Jul 28 18:56:59 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16114/RDF Added Files: ServiceInstanceRDF.pm InOutArticlesRDF.pm Log Message: added two new modules for generating RDF of MOBY-S Service Instances. This serves both the straight URL RDF documents, as well as (in a few minutes) the LSID metadata resolver service moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,NONE,1.1 InOutArticlesRDF.pm,NONE,1.1 From mwilkinson at pub.open-bio.org Wed Jul 28 22:59:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 18:59:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282259.i6SMxYGc016201@pub.open-bio.org> mwilkinson Wed Jul 28 18:59:34 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16178/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: clean up and add one more test moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.1,1.2 ServiceInstanceRDF.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:56:59 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:59:34 1.2 @@ -47,6 +47,7 @@ return 0 unless $args{'type'} && ( ($args{'type'} =~ /consumes/i) || ($args{'type'} =~ /produces/i) ); return 0 unless $args{'subject'} && (ref($args{'subject'}) =~ /rdf::core/i); return 0 unless $args{'araticles'} && (ref($args{'articles'}) =~ /array/i); + return 1 unless ${$args{'articles'}}[0]; # if there ARE no articles, this is a valid result! my $caller_is_obj = ref($caller); my $class = $caller_is_obj || $caller; @@ -134,13 +135,7 @@ my $namespaces = $ART->namespaces(); foreach (@{$namespaces}){ - # prime with base Object type "Class" - my $namespace = _addClassResource($model, NS, "$_", ''); - #my $type = $subject->new(RDF_NS,'type'); - #my $class = new RDF::Core::Resource(RDFS_NS,'Class'); - #my $statement = new RDF::Core::Statement($namespace, $type, $class); - #$model->addStmt($statement); - + my $namespace = _addClassResource($model, NS, "$_", ''); my $inNamespace = $article->new(MP, 'namespace_type'); my $statement = new RDF::Core::Statement($article, $inNamespace, $namespace); $model->addStmt($statement); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:56:59 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:59:34 1.2 @@ -69,16 +69,9 @@ _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title my $inputs = $service->input; - #my @inputs = @{$inputs}; my $outputs = $service->output; - #my @outputs = @{$outputs}; - -# THERE SHOULD BE A LOOP HERE TO TEST IF ANY INPUTS AT ALL - - - #foreach my $IN(@inputs){ my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', @@ -86,9 +79,6 @@ articles => $inputs, ); - #} -##################################################### - my $OutputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'produces', From mwilkinson at pub.open-bio.org Wed Jul 28 23:00:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:00:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282300.i6SN09fA016280@pub.open-bio.org> mwilkinson Wed Jul 28 19:00:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv16257 Modified Files: INSTALL MANIFEST Log Message: adding new modules to the manifest. removing old outdated installation documents moby-live/Perl INSTALL,1.1,1.2 MANIFEST,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/INSTALL 2003/06/10 17:12:52 1.1 +++ /home/repository/moby/moby-live/Perl/INSTALL 2004/07/28 23:00:09 1.2 @@ -1,33 +1,15 @@ ----------- CLIENT CONFIGURATION ---------- -If you wish to conect, by default, to anything other than -the MOBY Central registry running at the Canadian -Bioinformatics Resource (mobycentral.cbr.nrc.ca) then -you should set the following environment variables: +perl Makefile.PL +make +make install -MOBY_SERVER=http://your.favorite.server/cgi-bin/serverscriptname.pl -MOBY_URI=http://your.favorite.server/PathTo/MOBY -for example, to connect by default to a local copy of -the registry it might look like this: +MOST PEOPLE CAN STOP READING NOW! -MOBY_SERVER=http://localhost/cgi-bin/MOBY-Central.pl -MOBY_URI=http://localhost/MOBY/Central -=========================================== +For details on how to configure your own MOBY Central +registry, should you want to set one up (you DO NOT +need to set up a registry to acess nor service MOBY-S +Services) please visit the "Installing a Local Registy" +link on the biomoby.org homepage. -------- SERVER CONFIGURATION ------------ -If you are installing a local copy of MOBY Central -you will need to set some additional environment -variables in your httpd.conf file to tell the modules -where your mysql installation is. These are -configured using the apache SetEnv directive as follows: - -SetEnv MOBY_CENTRAL_DBNAME mobycentral -SetEnv MOBY_CENTRAL_DBPASS yourpassword -SetEnv MOBY_CENTRAL_DBPORT 3306 -SetEnv MOBY_CENTRAL_DBUSER mobyusername -SetEnv MOBY_CENTRAL_URL localhost - -(don't forget to restart your server...) -========================================== - +Mark =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MANIFEST 2004/06/24 22:32:38 1.11 +++ /home/repository/moby/moby-live/Perl/MANIFEST 2004/07/28 23:00:09 1.12 @@ -45,3 +45,5 @@ MOBY/lsid/authority/RelationshipResolver.pm MOBY/lsid/authority/ServiceInstanceResolver.pm MOBY/lsid/authority/ServiceResolver.pm +MOBY/RDF/ServiceInstanceRDF.pm +MOBY/RDF/InOutArticlesRDF.pm From mwilkinson at pub.open-bio.org Wed Jul 28 23:08:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:08:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282308.i6SN89Nu016375@pub.open-bio.org> mwilkinson Wed Jul 28 19:08:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16356/RDF Modified Files: ServiceInstanceRDF.pm Log Message: RDF/ServiceInstanceRDF.pm moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 22:59:34 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:08:09 1.3 @@ -1,6 +1,5 @@ package MOBY::RDF::ServiceInstanceRDF; use strict; -use lib '../../'; use MOBY::RDF::InOutArticlesRDF; require Exporter; our @ISA = qw(Exporter); @@ -50,7 +49,7 @@ sub build { my ($self) = @_; - my $service = $self->service; + my $service = $self->service_instance; my $model = $self->model; my $Bag = new RDF::Core::Resource(RDF_NS,'Bag'); From mwilkinson at pub.open-bio.org Wed Jul 28 23:12:11 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:12:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282312.i6SNCBj7016462@pub.open-bio.org> mwilkinson Wed Jul 28 19:12:11 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16439/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: shuffling subroutines around moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.2,1.3 ServiceInstanceRDF.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 22:59:34 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:12:11 1.3 @@ -141,4 +141,59 @@ $model->addStmt($statement); } } + + + +sub _addResource { + my ($model, $ns, $predicate, $subject, $ons, $object) = @_; + + $predicate = $subject->new($ns, $predicate); + $object = new RDF::Core::Resource($ons, $object); + my $statement = new RDF::Core::Statement($subject, $predicate, $object); + $model->addStmt($statement); + +} + + +# these should also be stripped out into their own module +sub _addClassResource { + my ($model, $ns, $thing, $def) = @_; + my ($subject, $statement, $class, $label, $type); + + $label = ($thing =~ /urn:lsid.*:(\S+)$/)?$1:$thing; + + unless (ref($thing) =~ /RDF/){ + $subject = new RDF::Core::Resource($ns, $thing); + } + + $type = $subject->new(RDF_NS,'type'); + $class = new RDF::Core::Resource(RDFS_NS,'Class'); + $statement = new RDF::Core::Statement($subject, $type, $class); + $model->addStmt($statement); + + $type = $subject->new(RDFS_NS,'label'); + $label = new RDF::Core::Literal($label,"en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject unless $def; + + $type = $subject->new(RDFS_NS,'comment'); + $label = new RDF::Core::Literal($def, "en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject; +} + +sub _addClassLiteral { + my ($model, $pns, $subject, $predicate, $value) = @_; + + $predicate = $subject->new($pns, $predicate); + $value = new RDF::Core::Literal($value, "en", "http://www.w3.org/2001/XMLSchema#string"); + my $statement = new RDF::Core::Statement($subject, $predicate, $value); + $model->addStmt($statement); + +} + 1; \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:08:09 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:12:11 1.4 @@ -88,4 +88,55 @@ } +# these should be stripped out into their own module... +sub _addResource { + my ($model, $ns, $predicate, $subject, $ons, $object) = @_; + + $predicate = $subject->new($ns, $predicate); + $object = new RDF::Core::Resource($ons, $object); + my $statement = new RDF::Core::Statement($subject, $predicate, $object); + $model->addStmt($statement); + +} + +sub _addClassResource { + my ($model, $ns, $thing, $def) = @_; + my ($subject, $statement, $class, $label, $type); + + $label = ($thing =~ /urn:lsid.*:(\S+)$/)?$1:$thing; + + unless (ref($thing) =~ /RDF/){ + $subject = new RDF::Core::Resource($ns, $thing); + } + + $type = $subject->new(RDF_NS,'type'); + $class = new RDF::Core::Resource(RDFS_NS,'Class'); + $statement = new RDF::Core::Statement($subject, $type, $class); + $model->addStmt($statement); + + $type = $subject->new(RDFS_NS,'label'); + $label = new RDF::Core::Literal($label,"en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject unless $def; + + $type = $subject->new(RDFS_NS,'comment'); + $label = new RDF::Core::Literal($def, "en", "http://www.w3.org/2001/XMLSchema#string"); + $statement = new RDF::Core::Statement($subject, $type, $label); + $model->addStmt($statement); + + return $subject; +} + +sub _addClassLiteral { + my ($model, $pns, $subject, $predicate, $value) = @_; + + $predicate = $subject->new($pns, $predicate); + $value = new RDF::Core::Literal($value, "en", "http://www.w3.org/2001/XMLSchema#string"); + my $statement = new RDF::Core::Statement($subject, $predicate, $value); + $model->addStmt($statement); + +} + 1; \ No newline at end of file From mwilkinson at pub.open-bio.org Wed Jul 28 23:41:39 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:41:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282341.i6SNfdka016576@pub.open-bio.org> mwilkinson Wed Jul 28 19:41:39 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16557/RDF Modified Files: InOutArticlesRDF.pm Log Message: adding a class variable counter for the various node factories so that all inputs in the database don't end up getting added to a single service in the RDF >>grin<< moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:12:11 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:41:39 1.4 @@ -1,6 +1,7 @@ package MOBY::RDF::InOutArticlesRDF; use strict; use RDF::Core::NodeFactory; +use RDF::Core::Statement; require Exporter; our @ISA = qw(Exporter); @@ -14,6 +15,35 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +{ + my $inputcounter = 1; + my $outputcounter = 1; + my $simplecounter = 1; + my $collectioncounter = 1; + + sub nextinput { + ++$inputcounter; + $inputcounter = 1 if $inputcounter==100000; + return $inputcounter; + } + sub nextoutput { + ++$outputcounter; + $outputcounter = 1 if $outputcounter==100000; + return $outputcounter; + } + sub nextsimple { + ++$simplecounter; + $simplecounter = 1 if $simplecounter==100000; + return $simplecounter; + } + sub nextcollection { + ++$collectioncounter; + $collectioncounter = 1 if $collectioncounter==100000; + return $collectioncounter; + } + +} + sub type { my ($self, @args) = @_; $args[0] && ($self->{type} = $args[0]); @@ -46,7 +76,7 @@ return 0 unless $args{'model'} && (ref($args{'model'}) =~ /rdf::core/i); return 0 unless $args{'type'} && ( ($args{'type'} =~ /consumes/i) || ($args{'type'} =~ /produces/i) ); return 0 unless $args{'subject'} && (ref($args{'subject'}) =~ /rdf::core/i); - return 0 unless $args{'araticles'} && (ref($args{'articles'}) =~ /array/i); + return 0 unless $args{'articles'} && (ref($args{'articles'}) =~ /array/i); return 1 unless ${$args{'articles'}}[0]; # if there ARE no articles, this is a valid result! my $caller_is_obj = ref($caller); @@ -61,10 +91,10 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &inputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &outputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &simplecounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &collectioncounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); @@ -91,8 +121,9 @@ my @articles = $self->articles; my $Bag = $self->{Bag}; - my $li = 1; + my $li = 0; foreach my $IN(@articles){ + ++$li; my $LI = $Thingy->new(RDF_NS, "_$li"); my $input = $self->{inputfactory}->newResource; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); @@ -111,9 +142,10 @@ _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; my $simps = $IN->Simples; + my $lli=0; foreach my $simp(@{$simps}){ - my $li = 1; - my $LI = $input->new(RDF_NS, "_$li"); + ++$lli; + my $LI = $input->new(RDF_NS, "_$lli"); my $collection_member = $self->{inputfactory}->newResource; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); From mwilkinson at pub.open-bio.org Wed Jul 28 23:45:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 19:45:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407282345.i6SNjXjY016644@pub.open-bio.org> mwilkinson Wed Jul 28 19:45:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16625/RDF Modified Files: InOutArticlesRDF.pm Log Message: call the method, not the variable moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:41:39 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:45:33 1.5 @@ -91,10 +91,10 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &inputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &outputcounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &simplecounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &collectioncounter(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &nextinput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &nextoutput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &nextsimple(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &nextcollection(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); From mwilkinson at pub.open-bio.org Thu Jul 29 00:22:21 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 20:22:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407290022.i6T0MLaF016803@pub.open-bio.org> mwilkinson Wed Jul 28 20:22:21 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv16780/MOBY/RDF Modified Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: ups. Got my class variables wrong. Now it increments properly to associate inputs with the correct services moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.5,1.6 ServiceInstanceRDF.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/28 23:45:33 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 00:22:21 1.6 @@ -16,30 +16,22 @@ use constant DC => 'http://purl.org/dc/elements/1.1/'; { - my $inputcounter = 1; - my $outputcounter = 1; - my $simplecounter = 1; - my $collectioncounter = 1; + my $inputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $outputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $simplefactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $collectionfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); sub nextinput { - ++$inputcounter; - $inputcounter = 1 if $inputcounter==100000; - return $inputcounter; + return $inputfactory->newResource } sub nextoutput { - ++$outputcounter; - $outputcounter = 1 if $outputcounter==100000; - return $outputcounter; + return $outputfactory->newResource } sub nextsimple { - ++$simplecounter; - $simplecounter = 1 if $simplecounter==100000; - return $simplecounter; + return $simplefactory->newResource } sub nextcollection { - ++$collectioncounter; - $collectioncounter = 1 if $collectioncounter==100000; - return $collectioncounter; + return $collectionfactory->newResource } } @@ -91,14 +83,14 @@ my $subject = $self->subject; my $model = $self->model; - $self->{inputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => &nextinput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{outputfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => &nextoutput(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{simplefactory} = new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => &nextsimple(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); - $self->{collectionfactory} = new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => &nextcollection(),BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); $self->{Bag} = new RDF::Core::Resource(RDF_NS,'Bag'); - - my $Thingy = $self->{inputfactory}->newResource; # create a bnode + my $Thingy; + if ($self->type eq 'consumes'){ + $Thingy = &nextinput; # create a bnode + } else { + $Thingy = &nextoutput; # create a bnode + } my $predicate = $subject->new(MP,$self->type); # 'consumes' or 'produces' my $statement = new RDF::Core::Statement($subject, $predicate, $Thingy); $model->addStmt($statement); @@ -125,13 +117,12 @@ foreach my $IN(@articles){ ++$li; my $LI = $Thingy->new(RDF_NS, "_$li"); - my $input = $self->{inputfactory}->newResource; + my $input = &nextsimple; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); $model->addStmt($statement); # # - - + if ($IN->isSimple){ &_addSimple($model, $input, $IN); } else { # COLLECTION @@ -146,7 +137,7 @@ foreach my $simp(@{$simps}){ ++$lli; my $LI = $input->new(RDF_NS, "_$lli"); - my $collection_member = $self->{inputfactory}->newResource; + my $collection_member = &nextcollection; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/28 23:12:11 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 00:22:21 1.5 @@ -1,6 +1,8 @@ package MOBY::RDF::ServiceInstanceRDF; use strict; use MOBY::RDF::InOutArticlesRDF; +use RDF::Core::Statement; + require Exporter; our @ISA = qw(Exporter); our @EXPORT_OK = qw(); From mwilkinson at pub.open-bio.org Thu Jul 29 00:36:55 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 28 Jul 2004 20:36:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407290036.i6T0atVS016900@pub.open-bio.org> mwilkinson Wed Jul 28 20:36:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv16881/MOBY/lsid/authority Modified Files: ServiceInstanceResolver.pm Log Message: the LSID resolver for service instance LSID's now uses the same modules as the RESOURCES script, and should output identically formatted RDF moby-live/Perl/MOBY/lsid/authority ServiceInstanceResolver.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm 2004/01/15 20:59:38 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/ServiceInstanceResolver.pm 2004/07/29 00:36:54 1.4 @@ -5,6 +5,35 @@ use XML::DOM; use MOBY::lsid::authority::RDFConfigure qw(:all); use MOBY::Client::Central; +use MOBY::RDF::ServiceInstanceRDF; + +use RDF::Core; +use RDF::Core::Model; +use RDF::Core::Literal; +use RDF::Core::Statement; +use RDF::Core::Model::Serializer; +use RDF::Core::Storage::Memory; +use RDF::Core::Constants qw(:xml :rdf :rdfs); +use constant OBJ => 'http://biomoby.org/RESOURCES/MOBY-S/Objects#'; +use constant SRV => 'http://biomoby.org/RESOURCES/MOBY-S/Services#'; +use constant NS => 'http://biomoby.org/RESOURCES/MOBY-S/Namespaces#'; +use constant MP => 'http://biomoby.org/RESOURCES/MOBY-S/Predicates#'; +use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; +use constant DC => 'http://purl.org/dc/elements/1.1/'; + +sub xmlNamespaces { + return { + RDF_NS() => 'rdf', + RDFS_NS() => 'rdfs', + OBJ() => 'mobyObject', + NS() => 'mobyNamespace', + SRV() => 'mobyService', + MP() => 'mobyPred', + SI() => 'serviceInstances', + DC() => 'dc', + } +} + @ISA = qw(Exporter); @EXPORT_OK = qw( @@ -14,8 +43,21 @@ resolve_ServiceInstance )]); +sub _serialize { + my ($model) = @_; + my $xml = ''; + + my $serializer = new RDF::Core::Model::Serializer( + Model=>$model, + Output=>\$xml, + getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! + ); + $serializer->serialize; + print "$xml\n"; +} sub resolve_ServiceInstance { + my ($ls) = @_; my $lsid= LS::ID->new($ls)->canonical; unless ($lsid) { @@ -37,175 +79,20 @@ unless ($si && ${$si}[0]){ _die('UNKNOWN_LSID'); } - my $service = shift(@{$si}); - # LSID is now fully validated. Carry on with metadata. - $RDF_PREFIX?1:1; - $mdata= $RDF_PREFIX; - - $mdata.= rdfLiteral( - $lsid->as_string, - 'rdf:type', # rdf:Type - 'i3csp:bioMobyService' - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:name', # i3c:Name - $service->name - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:title', # dc:Title - $service->name - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:label', # dc:Label - $service->name - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:publishedBy', # i3d:publishedBy - $service->authority - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:authoritative', # i3c:authoritative - $service->authoritative - ); - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:description', # i3c:description - $service->description - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'i3csp:endpoint', # i3c:endpoint - $service->URL - ); - - $mdata.= rdfLiteral( - $lsid->as_string, - 'dc:contributor', # dc:contributor - $service->contactEmail - ); - - $mdata.= rdfResource( - $lsid->as_string, - 'i3csp:performsTask', # i3csp:performsTask - 'urn:lsid:biomoby.org:servicetype:'.($service->type) - ); - - - my $inputs = $service->input; - my @inputs = @{$inputs}; + my $storage = new RDF::Core::Storage::Memory; + my $model = new RDF::Core::Model (Storage => $storage); - my $outputs = $service->output; - my @outputs = @{$outputs}; - - $mdata .= rdfBnode( - $lsid->as_string, - 'i3csp:primaryInput', # primaryInput bnode - 'primaryInput' - ); - my $in=0; - foreach (@inputs){ - ++$in; - $mdata .= rdfBnodeBnode( - 'primaryInput', - 'i3csp:primaryParameter', # primaryParameter bnode - "primaryParameter$in" - ); - $mdata .= rdfBnodeLiteral( - "primaryParameter$in", - 'i3csp:parameterName', - $_->articleName - ); - if ($_->isSimple){ - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterType', - 'i3csp:mobySimpleType' - ); - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($_->objectType) - ); - } else { - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterType', - 'i3csp:mobyCollectionType' - ); - my $simps = $_->Simples; - foreach my $simp(@{$simps}){ - $mdata .= rdfBnodeResource( - "primaryParameter$in", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($simp->objectType) - ); - } - } - } - - $mdata .= rdfBnode( - $lsid->as_string, - 'i3csp:primaryOutput', # primaryInput bnode - 'primaryOutput' - ); - my $out= $in; # switch for readability - foreach (@outputs){ - ++$out; - $mdata .= rdfBnodeBnode( - 'primaryOutput', - 'i3csp:primaryParameter', # primaryParameter bnode - "primaryParameter$out" - ); - $mdata .= rdfBnodeLiteral( - "primaryParameter$out", - 'i3csp:parameterName', - $_->articleName - ); - if ($_->isSimple){ - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterType', - 'i3csp:mobySimpleType' - ); - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($_->objectType) - ); - } else { - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterType', - 'i3csp:mobyCollectionType' - ); - my $simps = $_->Simples; - foreach my $simp(@{$simps}){ - $mdata .= rdfBnodeResource( - "primaryParameter$out", - 'i3csp:parameterClass', - 'urn:lsid:biomoby.org:objectclass:'.($simp->objectType) - ); - } - } + foreach my $service(@{$si}){ + my $ServInstRDF = MOBY::RDF::ServiceInstanceRDF->new( + model => $model, + service_instance => $service, + ); } - - # +++++++++++ now we need the secondaries ++++++++ - $mdata.= $RDF_SUFFIX; - $RDF_SUFFIX?1:1; - - unless ($mdata) { - _die ('NO_METADATA_AVAILABLE'); - } - return $mdata; + print header(-type => 'application/rdf+xml', -expires => 'now'); + _serialize($model); + exit 1; } + +1; From mwilkinson at pub.open-bio.org Thu Jul 29 16:11:41 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 12:11:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407291611.i6TGBfMA019343@pub.open-bio.org> mwilkinson Thu Jul 29 12:11:40 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv19324/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: adding support for secondaries into the RDF generating routines moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 00:22:21 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 16:11:40 1.7 @@ -15,11 +15,13 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; -{ +{ # these need to be class variables, since this module is loaded multiple times, but the newResouce counter has to increment nevertheless. + my $inputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:input', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $outputfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:output', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $simplefactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:simple', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); my $collectionfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:collection', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); + my $secondaryfactory ||= new RDF::Core::NodeFactory( GenPrefix => '_:secondary', GenCounter => 0,BaseURI=>'http://www.biomoby.org/nil');# BaseURI=>'http://www.foo.org/'); sub nextinput { return $inputfactory->newResource @@ -33,9 +35,14 @@ sub nextcollection { return $collectionfactory->newResource } + sub nextsecondary { + return $secondaryfactory->newResource + } } + + sub type { my ($self, @args) = @_; $args[0] && ($self->{type} = $args[0]); @@ -116,7 +123,7 @@ my $li = 0; foreach my $IN(@articles){ ++$li; - my $LI = $Thingy->new(RDF_NS, "_$li"); + my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc my $input = &nextsimple; my $statement = new RDF::Core::Statement($Thingy, $LI, $input); $model->addStmt($statement); @@ -125,18 +132,18 @@ if ($IN->isSimple){ &_addSimple($model, $input, $IN); - } else { # COLLECTION + } elsif ($IN->isCollection) { # COLLECTION - is just a bag of simples my $type = $input->new(RDF_NS,'type'); my $statement = new RDF::Core::Statement($input, $type, $Bag); $model->addStmt($statement); # - _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; + _addClassLiteral($model, MP, $input, 'articleName', $IN->articleName) if $IN->articleName; # the bag has an articlename my $simps = $IN->Simples; my $lli=0; foreach my $simp(@{$simps}){ ++$lli; - my $LI = $input->new(RDF_NS, "_$lli"); + my $LI = $input->new(RDF_NS, "_$lli"); # nodes - need to be numbered :_1, :_2, etc; these connect to the individual simples my $collection_member = &nextcollection; my $statement = new RDF::Core::Statement($input, $LI, $collection_member); $model->addStmt($statement); @@ -144,6 +151,10 @@ &_addSimple($model, $collection_member, $simp); } + } elsif ($IN->isSecondary) { + &_addSecondary($model, $input, $IN); + } else { + print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; } } } @@ -166,6 +177,27 @@ } +#| secondary_input_id | int(10) unsigned | | PRI | NULL | auto_increment | +#| default_value | text | YES | | NULL | | +#| maximum_value | decimal(10,0) | YES | | NULL | | +#| minimum_value | decimal(10,0) | YES | | NULL | | +#| enum_value | text | YES | | NULL | | +#| datatype | enum('String','Integer','DateTime','Float') | YES | | NULL | | +#| article_name | varchar(255) | YES | | NULL | | +#| service_instance_id | int(10) unsigned | | | 0 | | +sub _addSecondary { + my ($model, $article, $ART) = @_; # (RDF::COre::Model, $RDF::Core::Resource, $MOBY::Client::SimpleArticle) + _addClassLiteral($model, MP, $article, 'article_name', $ART->articleName) if $ART->articleName; + _addClassLiteral($model, MP, $article, 'default_value', $ART->default) if $ART->default; + _addClassLiteral($model, MP, $article, 'datatype', $ART->datatype) if $ART->datatype; + _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; + _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; + my @enums = $ART->enum; + foreach (@enums){ + _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; + } + +} sub _addResource { my ($model, $ns, $predicate, $subject, $ons, $object) = @_; From mwilkinson at pub.open-bio.org Thu Jul 29 17:49:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 13:49:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407291749.i6THnIfq019710@pub.open-bio.org> mwilkinson Thu Jul 29 13:49:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory pub.open-bio.org:/tmp/cvs-serv19691/MOBY/lsid/authority Modified Files: metadata.pl Log Message: LSID's are no longer case sensitive in the new LS::* stack from IBM moby-live/Perl/MOBY/lsid/authority metadata.pl,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl 2004/01/15 20:59:38 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/metadata.pl 2004/07/29 17:49:18 1.5 @@ -28,13 +28,13 @@ use MOBY::lsid::authority::ServiceInstanceResolver qw(:all); my %known_types = ( # switch on/off various LSID-namespace resolvers. - 'namespacetype' => 1, - 'objectclass' => 1, - 'servicetype' => 1, - 'servicerelation' => 1, - 'objectrelation' => 1, - 'serviceinstance' => 1, - 'rdfpredicate' => 1, + 'NamespaceType' => 1, + 'ObjectClass' => 1, + 'ServiceType' => 1, + 'ServiceRelation' => 1, + 'ObjectRelation' => 1, + 'ServiceInstance' => 1, + 'MOBYSPredicate' => 1, ); MetaData(); @@ -68,13 +68,13 @@ _die("UNKNOWN_LSID"); } - return resolve_namespacetype($namespacedb,$lsid) if $1 eq "namespacetype"; - return resolve_classtype($objectdb,$lsid) if $1 eq "objectclass"; - return resolve_servicetype($servicedb,$lsid) if $1 eq "servicetype"; - return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "objectrelation"; - return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "servicerelation"; - return resolve_mobyPredicate($lsid) if $1 eq "rdfpredicate"; - return resolve_ServiceInstance($lsid) if $1 eq "serviceinstance"; + return resolve_namespacetype($namespacedb,$lsid) if $1 =~ /namespacetype/i; + return resolve_classtype($objectdb,$lsid) if $1 =~ /objectclass/i; + return resolve_servicetype($servicedb,$lsid) if $1 =~ /servicetype/i; + return resolve_relationshiptype($relationshipdb,$lsid) if $1 =~ /objectrelation/i; + return resolve_relationshiptype($relationshipdb,$lsid) if $1 =~ /servicerelation/i; + return resolve_mobyPredicate($lsid) if $1 =~ /rdfpredicate/i; + return resolve_ServiceInstance($lsid) if $1 =~ /serviceinstance/i; } From mwilkinson at pub.open-bio.org Thu Jul 29 21:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 17:53:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrsHH020286@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY/Client Modified Files: Central.pm Registration.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY/Client Central.pm,1.76,1.77 Registration.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.76 retrieving revision 1.77 diff -u -r1.76 -r1.77 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/06/16 01:15:30 1.76 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/29 21:53:54 1.77 @@ -1654,10 +1654,12 @@ my $id = &_nodeTextContent($Object, 'id'); my $success = &_nodeTextContent($Object, 'success'); my $message = &_nodeTextContent($Object, 'message'); + my $RDF = &_nodeTextContent($Object, 'RDF'); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, registration_id => $id, + RDF => $RDF, id => $id); return $reg; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2003/06/06 00:45:47 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/07/29 21:53:54 1.5 @@ -81,6 +81,7 @@ success => [0, 'read/write'], message => ["OK", 'read/write'], registration_id => [undef, 'read/write'], + RDF => [undef, 'read/write'], ); #_____________________________________________________________ From mwilkinson at pub.open-bio.org Thu Jul 29 21:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 17:53:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrsB1020305@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:54 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 00:22:21 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 21:53:54 1.6 @@ -15,6 +15,33 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +sub xmlNamespaces { + return { + RDF_NS() => 'rdf', + RDFS_NS() => 'rdfs', + OBJ() => 'mobyObject', + NS() => 'mobyNamespace', + SRV() => 'mobyService', + MP() => 'mobyPred', + SI() => 'serviceInstances', + DC() => 'dc', + } +} + + +sub serialize { + my ($model) = @_; + my $xml = ''; + + my $serializer = new RDF::Core::Model::Serializer( + Model=>$model, + Output=>\$xml, + getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! + ); + $serializer->serialize; + return $xml; +} + sub model { my ($self, @args) = @_; $args[0] && ($self->{model} = $args[0]); From mwilkinson at pub.open-bio.org Thu Jul 29 21:53:54 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 17:53:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292153.i6TLrspw020263@pub.open-bio.org> mwilkinson Thu Jul 29 17:53:53 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv20244/MOBY Modified Files: Central.pm Log Message: currently untested. This should now return RDF of the service signature to a client who registers a service. IF this works, and is parsable by Nina's agent, we will switch off service deregistration shortly and send an RDF message to everyone with a registered service moby-live/Perl/MOBY Central.pm,1.133,1.134 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.133 retrieving revision 1.134 diff -u -r1.133 -r1.134 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/12 00:39:37 1.133 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 21:53:53 1.134 @@ -22,6 +22,14 @@ use MOBY::secondary_input; use MOBY::central_db_connection; use MOBY::Config; +use MOBY::RDF::ServiceInstanceRDF; +use RDF::Core; +use RDF::Core::Model; +use RDF::Core::Literal; +use RDF::Core::Statement; +use RDF::Core::Model::Serializer; +use RDF::Core::Storage::Memory; +use RDF::Core::Constants qw(:xml :rdf :rdfs); my $debug = 0; @@ -153,11 +161,15 @@ my $id = $details->{id}; my $success = $details->{success}; my $message = $details->{message}; + my $RDF = ""; + $RDF = $details->{RDF}; + return " $id $success + "; } @@ -1149,7 +1161,36 @@ return &_error("Registration Failed During SECONDARY Article Registration: $msg","") unless ($success==1); } - return &_success("Registration successful", $SVC->service_instance_id); + # we're going to do a findService here to find the service that we just created + # and use the resulting XML to create a MOBY::Client::ServiceInstance object + # that we can then use to retrieve the RDF for that service signature. + # this is roundabout, I agree, but it is the most re-usable way to go at + # the moment. + + my ($si, $reg) = &findService(qw{ + + + $AuthURI; + $serviceName; + + "}); + unless ($si){ + $SVC->DELETE_THYSELF; + return &_error("Registration Failed - newly registered service could not be discovered",""); + } + my $service = shift @{$si}; + unless ($service){ + $SVC->DELETE_THYSELF; + return &_error("Registration Failed - newly registered service could not be discovered",""); + } + + my $services = MOBY::Client::Central::_parseServices('', '', $service); + my $service_instance = shift @{$services}; + my $storage = new RDF::Core::Storage::Memory; + my $model = new RDF::Core::Model (Storage => $storage); + my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(model => $model, service_instance => $service_instance); + my $RDF_XML = $RDF_MODEL->serialize; + return &_success("Registration successful", $SVC->service_instance_id, $RDF_XML); } sub _registerArticles { @@ -2977,11 +3018,12 @@ } sub _success { - my ($message, $id) = @_; + my ($message, $id, $RDF) = @_; my $reg = &Registration({ success => 1, message => "$message", id => "$id", + RDF => $RDF, }); return $reg; } From gss at pub.open-bio.org Thu Jul 29 23:30:12 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:30:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292330.i6TNUCwS020618@pub.open-bio.org> gss Thu Jul 29 19:30:12 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test In directory pub.open-bio.org:/tmp/cvs-serv20593/src/org/smoby/parser/test Modified Files: Test.java Log Message: Removed unused import statement moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java 2004/06/16 23:29:32 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java 2004/07/29 23:30:12 1.3 @@ -4,7 +4,6 @@ import java.util.*; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.parser.*; import com.hp.hpl.jena.rdf.model.*; From gss at pub.open-bio.org Thu Jul 29 23:31:44 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:31:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292331.i6TNViBj020675@pub.open-bio.org> gss Thu Jul 29 19:31:44 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl In directory pub.open-bio.org:/tmp/cvs-serv20626/src/org/smoby/graph/impl Removed Files: MOBYProviderSetImpl.java MOBYProviderImpl.java MOBYResizableCollectionImpl.java MOBYUnorderedCollectionImpl.java MOBYDateConstraintImpl.java MOBYPropertyValueStatementImpl.java MOBYDocumentImpl.java MOBYLiteralImpl.java MOBYOntologyImpl.java MOBYEnumerationImpl.java MOBYSubjectImpl.java MOBYGraphNodeImpl.java MOBYObjectFactory.java MOBYFixedCollectionImpl.java MOBYIntegerConstraintImpl.java MOBYObjectImpl.java MOBYPropertyValueConstraintImpl.java MOBYPropertyValueImpl.java MOBYMappingElementImpl.java MOBYGraphImpl.java MOBYNonPositiveIntegerConstraintImpl.java MOBYNumericConstraintImpl.java MOBYNonNegativeIntegerConstraintImpl.java MOBYOrderedCollectionImpl.java MOBYResourceImpl.java MOBYDescriptorImpl.java MOBYCollectionImpl.java MOBYSingleElementImpl.java Log Message: No longer separate graph interfaces from classes moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderSetImpl.java,1.1,NONE MOBYProviderImpl.java,1.2,NONE MOBYResizableCollectionImpl.java,1.2,NONE MOBYUnorderedCollectionImpl.java,1.2,NONE MOBYDateConstraintImpl.java,1.1,NONE MOBYPropertyValueStatementImpl.java,1.1,NONE MOBYDocumentImpl.java,1.2,NONE MOBYLiteralImpl.java,1.1,NONE MOBYOntologyImpl.java,1.2,NONE MOBYEnumerationImpl.java,1.2,NONE MOBYSubjectImpl.java,1.2,NONE MOBYGraphNodeImpl.java,1.2,NONE MOBYObjectFactory.java,1.3,NONE MOBYFixedCollectionImpl.java,1.2,NONE MOBYIntegerConstraintImpl.java,1.1,NONE MOBYObjectImpl.java,1.2,NONE MOBYPropertyValueConstraintImpl.java,1.1,NONE MOBYPropertyValueImpl.java,1.1,NONE MOBYMappingElementImpl.java,1.2,NONE MOBYGraphImpl.java,1.2,NONE MOBYNonPositiveIntegerConstraintImpl.java,1.1,NONE MOBYNumericConstraintImpl.java,1.1,NONE MOBYNonNegativeIntegerConstraintImpl.java,1.1,NONE MOBYOrderedCollectionImpl.java,1.2,NONE MOBYResourceImpl.java,1.1,NONE MOBYDescriptorI! mpl.java,1.2,NONE MOBYCollectionImpl.java,1.2,NONE MOBYSingleElementImpl.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYProviderSetImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYProviderImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYResizableCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYUnorderedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDateConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueStatementImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDocumentImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYLiteralImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYOntologyImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYEnumerationImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYSubjectImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYGraphNodeImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYObjectFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYFixedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYObjectImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYPropertyValueImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYMappingElementImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYGraphImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNonPositiveIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNumericConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYNonNegativeIntegerConstraintImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYOrderedCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYResourceImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYDescriptorImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYCollectionImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/MOBYSingleElementImpl.java,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 23:33:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:33:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292333.i6TNXxG9020829@pub.open-bio.org> gss Thu Jul 29 19:33:59 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph In directory pub.open-bio.org:/tmp/cvs-serv20716/src/org/smoby/graph Modified Files: MOBYDocument.java MOBYLiteral.java MOBYResource.java MOBYFixedCollection.java MOBYResizableCollection.java MOBYSingleElement.java MOBYPropertyValueConstraint.java MOBYPropertyValueStatement.java MOBYEnumeration.java MOBYProvider.java MOBYPropertyValue.java MOBYOntology.java MOBYProviderSet.java MOBYMappingElement.java MOBYDescriptor.java MOBYOrderedCollection.java MOBYCollection.java MOBYUnorderedCollection.java MOBYGraph.java MOBYGraphNode.java MOBYObject.java MOBYSubject.java MOBYPropertyValueException.java Added Files: MOBYIntegerConstraint.java MOBYDateConstraint.java MOBYNonNegativeIntegerConstraint.java MOBYNumericConstraint.java MOBYNonPositiveIntegerConstraint.java Log Message: No longer separate graph interfaces from classes moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYIntegerConstraint.java,NONE,1.1 MOBYDateConstraint.java,NONE,1.1 MOBYNonNegativeIntegerConstraint.java,NONE,1.1 MOBYNumericConstraint.java,NONE,1.1 MOBYNonPositiveIntegerConstraint.java,NONE,1.1 MOBYDocument.java,1.1,1.2 MOBYLiteral.java,1.1,1.2 MOBYResource.java,1.1,1.2 MOBYFixedCollection.java,1.1,1.2 MOBYResizableCollection.java,1.1,1.2 MOBYSingleElement.java,1.1,1.2 MOBYPropertyValueConstraint.java,1.1,1.2 MOBYPropertyValueStatement.java,1.1,1.2 MOBYEnumeration.java,1.1,1.2 MOBYProvider.java,1.1,1.2 MOBYPropertyValue.java,1.1,1.2 MOBYOntology.java,1.1,1.2 MOBYProviderSet.java,1.1,1.2 MOBYMappingElement.java,1.1,1.2 MOBYDescriptor.java,1.2,1.3 MOBYOrderedCollection.java,1.1,1.2 MOBYCollection.java,1.1,1.2 MOBYUnorderedCollection.java,1.1,1.2 MOBYGraph.java,1.1,1.2 MOBYGraphNode.java,1.1,1.2 MOBYObject.java,1.1,1.2 MOBYSubject.java,1.1,1.2 MOBYPropertyValueException.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDocument.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,15 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents a document to be incorporated into + * This class represents a document to be incorporated into * the S-MOBY metadata repository. */ -public interface MOBYDocument extends MOBYDescriptor +public abstract class MOBYDocument extends MOBYDescriptor { + public MOBYDocument(Resource resource, Model underlying) + { + super(resource, underlying); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYLiteral.java 2004/07/29 23:33:59 1.2 @@ -1,7 +1,24 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.Literal; -public interface MOBYLiteral extends MOBYPropertyValue +public class MOBYLiteral extends MOBYPropertyValue { - public String getStringValue(); -} \ No newline at end of file + private String stringValue; + + public MOBYLiteral(String stringValue) { + this.stringValue = stringValue; + } + + public String getStringValue() { + return stringValue; + } + + public boolean isLiteral() { + return true; + } + + public boolean isResource() { + return false; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResource.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,29 @@ package org.smoby.graph; +import org.smoby.graph.*; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYResource extends MOBYPropertyValue +public class MOBYResource extends MOBYPropertyValue { - public String getResourceURI(); - public boolean isBlank(); + private Resource resourceValue; + + public MOBYResource(Resource resourceValue) { + this.resourceValue = resourceValue; + } + + public String getResourceURI() { + return resourceValue.getURI(); + } + + public boolean isLiteral() { + return false; + } + + public boolean isResource() { + return true; + } + + public boolean isBlank() { + return resourceValue.isAnon(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYFixedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,20 @@ package org.smoby.graph; +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface representing unordered, fixed sized collection + * A class representing unordered, fixed sized collection * of objects. */ -public interface MOBYFixedCollection extends MOBYCollection +public class MOBYFixedCollection extends MOBYCollection { -} \ No newline at end of file + + public MOBYFixedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isResizable() { return false; } + public boolean isFixedSized() { return true; } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYResizableCollection.java 2004/07/29 23:33:59 1.2 @@ -1,14 +1,29 @@ package org.smoby.graph; +import java.util.*; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface representing collections that can be resized (i.e. + * A class representing collections that can be resized (i.e. * elements added to or removed from); such collections can be * either ordered or unordered. */ -public interface MOBYResizableCollection extends MOBYCollection +public abstract class MOBYResizableCollection extends MOBYCollection { + public MOBYResizableCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + /** * Return whether or not this collection is ordered. */ - public boolean isOrdered(); -} \ No newline at end of file + public abstract boolean isOrdered(); + + public boolean isResizable() { return true; } + public boolean isFixedSized() { return false; } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSingleElement.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,23 @@ package org.smoby.graph; +import java.net.URI; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface to represent singular objects, i.e. those that are + * A class to represent singular objects, i.e. those that are * not collections. */ -public interface MOBYSingleElement extends MOBYGraphNode +public abstract class MOBYSingleElement extends MOBYGraphNode { -} + public MOBYSingleElement(Resource resource, Model underlying) + { + super(resource, underlying); + } + + public boolean isSingular() { return true; } + public boolean isCollection() { return false; } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueConstraint.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,9 @@ package org.smoby.graph; -public interface MOBYPropertyValueConstraint +public abstract class MOBYPropertyValueConstraint { - public void validatePropertyValue(MOBYPropertyValueStatement stmt, - MOBYPropertyValue newValue) + public abstract void validatePropertyValue( + MOBYPropertyValueStatement stmt, + MOBYPropertyValue newValue) throws MOBYPropertyValueException; } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueStatement.java 2004/07/29 23:33:59 1.2 @@ -1,28 +1,76 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYPropertyValueStatement +public class MOBYPropertyValueStatement extends MOBYDescriptor { + private Statement jenaStatement; + private MOBYPropertyValue currentValue; + private MOBYPropertyValueConstraint constraint; + + public MOBYPropertyValueStatement(Statement jenaStatement, + Model underlying) { + super(null, underlying); + this.jenaStatement = jenaStatement; + if (jenaStatement.getObject().canAs(Resource.class)) { + Resource value = (Resource) jenaStatement.getObject(); + currentValue = new MOBYResource(value); + } else { + Literal value = (Literal) jenaStatement.getObject(); + currentValue = new MOBYLiteral(value.getString()); + } + } + /** * Return the name of this property */ - public String getPropertyName(); + public String getPropertyName() { + return jenaStatement.getPredicate().getURI(); + } + public String toString() { + return jenaStatement.toString(); + } + /** * Return the value currently associated with this property */ - public MOBYPropertyValue getValue(); - + public MOBYPropertyValue getValue() { + return currentValue; + } + /** * Set the property value. This is just a placeholder; values of * different property types will be set to different types of * values. */ public void setPropertyValue(MOBYPropertyValue newValue) - throws MOBYPropertyValueException; - + throws MOBYPropertyValueException + { + if (constraint != null) { + constraint.validatePropertyValue(this, newValue); + } + + if (newValue.isLiteral()) { + MOBYLiteral literal = (MOBYLiteral) newValue; + jenaStatement.changeObject(literal.getStringValue()); + } else { + MOBYResource resource = (MOBYResource) newValue; + if (resource.isBlank()) { + jenaStatement.changeObject( + jenaStatement.getModel().createResource()); + } else { + jenaStatement.changeObject( + jenaStatement.getModel().createResource( + resource.getResourceURI())); + } + } + } + /** * Set the given constraint for this property value statement */ - public void setConstraint(MOBYPropertyValueConstraint constraint); -} \ No newline at end of file + public void setConstraint(MOBYPropertyValueConstraint constraint) { + this.constraint = constraint; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYEnumeration.java 2004/07/29 23:33:59 1.2 @@ -1,10 +1,19 @@ package org.smoby.graph; +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface representing a resizable collection of objects, in + * A class representing a resizable collection of objects, in * which the order of the elements is not defined; the intention is * for the elements to represent possible choices for a value. */ -public interface MOBYEnumeration extends MOBYUnorderedCollection +public class MOBYEnumeration extends MOBYUnorderedCollection { -} + public MOBYEnumeration(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isEnumeration() { return true; } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProvider.java 2004/07/29 23:33:59 1.2 @@ -1,38 +1,84 @@ package org.smoby.graph; import java.io.*; +import com.hp.hpl.jena.rdf.model.*; /** - * The Provider interface represents a resource that provides a + * The Provider class represents a resource that provides a * service in MOBY. */ -public interface MOBYProvider extends MOBYDocument +public class MOBYProvider extends MOBYDocument { + private String name; + private String oneLineDescription; + private String moreInfoURI; + private MOBYUnorderedCollection operatesOn; + + public MOBYProvider(Resource resource, String name, String oneLineDescription, + String moreInfoURI, MOBYUnorderedCollection operatesOn, + Model underlying) + { + super(resource, underlying); + this.name = name; + this.oneLineDescription = oneLineDescription; + this.moreInfoURI = moreInfoURI; + this.operatesOn = operatesOn; + } + /** * Return a descriptive name for the provider. */ - public String getName(); - + public String getName() + { + return name; + } + /** * Return a short (one line) description for the provider. */ - public String getOneLineDescription(); - + public String getOneLineDescription() + { + return oneLineDescription; + } + /** * Return a URI that can be accessed to obtain more information * about the provider. */ - public String getMoreInfoURI(); + public String getMoreInfoURI() + { + return moreInfoURI; + } /** * Return a collection of graph nodes that this provider operates on. * Each graph node represents either a Graph or GraphCollection. */ - public MOBYUnorderedCollection getOperatesOn(); + public MOBYUnorderedCollection getOperatesOn() + { + return operatesOn; + } + public String toString() + { + StringBuffer sb = new StringBuffer(); + sb.append("Provider [name=\""); + sb.append(name); + sb.append("\", oneLineDescription=\""); + sb.append(oneLineDescription); + sb.append("\", moreInfoURI="); + sb.append(moreInfoURI); + sb.append("\"]"); + + return sb.toString(); + } + /** - * Provider implementations should be capable of serializing themselves + * Providers should be capable of serializing themselves * to an output stream */ - public void serialize(OutputStream out); -} \ No newline at end of file + public void serialize(OutputStream out) + { + underlying.write(out); + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValue.java 2004/07/29 23:33:59 1.2 @@ -1,18 +1,22 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.Model; + /** - * A superinterface for things that can appear as the subject + * A superclass for things that can appear as the subject * or object of a statement. */ -public interface MOBYPropertyValue +public abstract class MOBYPropertyValue { /** - * Return whether or not this property value represents a literal + * Return whether or not this property value represents + * a literal value */ - public boolean isLiteral(); - + public abstract boolean isLiteral(); + /** - * Return whether or not this property value represents a resource + * Return whether or not this property value represents + * a resource */ - public boolean isResource(); + public abstract boolean isResource(); } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOntology.java 2004/07/29 23:33:59 1.2 @@ -1,9 +1,14 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents a collection of RDF statements to be + * This class represents a collection of RDF statements to be * incorporated into the S-MOBY metadata repository. */ -public interface MOBYOntology extends MOBYDocument +public class MOBYOntology extends MOBYDocument { -} + public MOBYOntology(Resource resource, Model underlying) { + super(resource, underlying); + } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java 2004/06/18 21:37:52 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYProviderSet.java 2004/07/29 23:33:59 1.2 @@ -1,25 +1,56 @@ package org.smoby.graph; import java.io.*; +import java.util.*; +import org.smoby.tools.*; +import com.hp.hpl.jena.rdf.model.*; /** - * An interface to represent a set of providers + * An class to represent a set of providers */ -public interface MOBYProviderSet extends MOBYDocument +public class MOBYProviderSet extends MOBYDocument { + private List providers = new ArrayList(); + + public MOBYProviderSet() + { + super(null, null); + } + /** - * Add a provider to the set + * Return the size of the set */ - public void addProvider(MOBYProvider provider); - + public int size() + { + return providers.size(); + } + /** - * Return the size of the set + * Add a provider to the set */ - public int size(); - + public void addProvider(MOBYProvider provider) + { + providers.add(provider); + } + /** * Provider sets should be capable of serializing themselves * to an output stream */ - public void serialize(OutputStream out); + public void serialize(OutputStream out) + { + Model merged = ModelFactory.createDefaultModel(); + + for (Iterator it = providers.iterator(); it.hasNext();) + { + MOBYProvider provider = (MOBYProvider) it.next(); + Model underlying = provider.getUnderlying(); + merged.add(underlying); + merged.setNsPrefixes(underlying.getNsPrefixMap()); + } + + Util.removeUnusedNsPrefixes(merged); + + merged.write(out); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYMappingElement.java 2004/07/29 23:33:59 1.2 @@ -1,17 +1,36 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; -public interface MOBYMappingElement extends MOBYSingleElement + +public class MOBYMappingElement extends MOBYSingleElement { + private MOBYFixedCollection statements; + private MOBYCollection nestedElements; + + public MOBYMappingElement(Resource resource, MOBYFixedCollection statements, + MOBYCollection nestedElements, Model underlying) + { + super(resource, underlying); + this.statements = statements; + this.nestedElements = nestedElements; + } + /** * Return the collection of property-setting statements associated - * with this subject. + * with this mapping element. */ - public MOBYFixedCollection getPropertyValueStatements(); - + public MOBYFixedCollection getPropertyValueStatements() + { + return statements; + } + /** - * Return the collection of mappings that are nested within this subject - * through its role as a data structure. + * Return the collection of mappings that are nested within this + * mapping element through its role as a data structure. */ - public MOBYCollection getNestedElements(); + public MOBYCollection getNestedElements() { + return nestedElements; + } + } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/19 18:21:36 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYDescriptor.java 2004/07/29 23:33:59 1.3 @@ -1,17 +1,43 @@ package org.smoby.graph; -import java.net.URI; - -import com.hp.hpl.jena.rdf.model.Resource; +import com.hp.hpl.jena.rdf.model.*; /** - * The Resource interface represents things that are available + * The MOBYDescriptor class represents things that are available * at a URI. */ -public interface MOBYDescriptor +public abstract class MOBYDescriptor { + protected Model underlying; + protected Resource resource; + + public MOBYDescriptor(Resource resource, Model underlying) + { + this.resource = resource; + this.underlying = underlying; + } + + /** + * Return the resource associated with this descriptor. + */ + public Resource getResource() + { + return resource; + } + + /** + * Return the underlying Jena model + */ + public Model getUnderlying() + { + return underlying; + } + /** - * Return the URI represented by this node. + * Return the URI of the underlying resource, if any. */ - public Resource getResource(); -} + public String getURI() + { + return (resource == null) ? null : resource.getURI(); + } +} \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYOrderedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,13 +1,22 @@ package org.smoby.graph; -/** - * An interface representing resizable collection of objects, in - * which the order of the elements is defined. - */ -public interface MOBYOrderedCollection extends MOBYResizableCollection +import java.util.*; +import com.hp.hpl.jena.rdf.model.*; + +public class MOBYOrderedCollection extends MOBYResizableCollection { + public MOBYOrderedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isOrdered() { return true; } + /** * Return the object at a given zero-based index. */ - public Object get(int index); + public Object get(int index) + { + return elements.get(index); + } } =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYCollection.java 2004/07/29 23:33:59 1.2 @@ -1,30 +1,50 @@ package org.smoby.graph; -import java.util.Iterator; +import com.hp.hpl.jena.rdf.model.*; +import java.util.*; /** - * A common interface for collections, both fixed sized and resizeable, of - * elements in MOBY graphs. + * A common abstract class for collections, both fixed sized and resizeable, + * of elements in MOBY graphs. */ -public interface MOBYCollection extends MOBYGraphNode +public abstract class MOBYCollection extends MOBYGraphNode { + protected List elements = new ArrayList(); + + public MOBYCollection(Resource resource, List elements, Model underlying) + { + super(resource, underlying); + for (Iterator it = elements.iterator(); it.hasNext();) { + this.elements.add(it.next()); + } + } + /** - * Return whether or not the collection is fixed in size + * Return the size of the collection. */ - public boolean isFixedSized(); - + public int size() + { + return elements.size(); + } + /** - * Return whether or not the collection is resizable + * Return an iterator for traversing the elements */ - public boolean isResizable(); + public Iterator iterator() + { + return elements.iterator(); + } /** - * Return an iterator for traversing the elements + * Return whether or not the collection is fixed in size */ - public Iterator iterator(); + public abstract boolean isFixedSized(); /** - * Return the size of the collection. + * Return whether or not the collection is resizable */ - public int size(); + public abstract boolean isResizable(); + + public boolean isSingular() { return false; } + public boolean isCollection() { return true; } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYUnorderedCollection.java 2004/07/29 23:33:59 1.2 @@ -1,14 +1,28 @@ package org.smoby.graph; +import java.util.*; + +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; + /** - * An interface representing resizable collection of objects, in + * A class representing resizable collection of objects, in * which the order of the elements is not defined. */ -public interface MOBYUnorderedCollection extends MOBYResizableCollection +public class MOBYUnorderedCollection extends MOBYResizableCollection { + public MOBYUnorderedCollection(Resource resource, List elements, Model underlying) + { + super(resource, elements, underlying); + } + + public boolean isOrdered() { return false; } + /** * Return whether or not the elements of this collection represent * choices (i.e. elements of an enumeration of possible values). */ - public boolean isEnumeration(); + public boolean isEnumeration() { return false; } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraph.java 2004/07/29 23:33:59 1.2 @@ -1,13 +1,26 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * This interface represents singular (i.e. not collection) subgraphs + * This class represents singular (i.e. not collection) subgraphs * that have a single mapping. */ -public interface MOBYGraph extends MOBYSingleElement +public class MOBYGraph extends MOBYSingleElement { + private MOBYGraphNode hasMapping; + + public MOBYGraph(Resource resource, MOBYGraphNode hasMapping, Model underlying) + { + super(resource, underlying); + this.hasMapping = hasMapping; + } + /** * Return the object of this graph's hasMapping property. */ - public MOBYGraphNode gethasMapping(); + public MOBYGraphNode getHasMapping() + { + return hasMapping; + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYGraphNode.java 2004/07/29 23:33:59 1.2 @@ -1,23 +1,33 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** - * An interface for nodes in an RDF graph; these nodes are either + * An abstract class for nodes in an RDF graph; these nodes are either * collections or singular elements. */ -public interface MOBYGraphNode extends MOBYDescriptor +public abstract class MOBYGraphNode extends MOBYDescriptor { + public MOBYGraphNode(Resource resource, Model underlying) + { + super(resource, underlying); + } + /** * Return whether or not this node represents a blank node */ - public boolean isBlank(); + public boolean isBlank() + { + return (resource == null) || (resource.getURI() == null); + } /** * Return whether or not this object is a collection. */ - public boolean isCollection(); + public abstract boolean isCollection(); /** * Return whether or not this object is a singular element. */ - public boolean isSingular(); + public abstract boolean isSingular(); } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYObject.java 2004/07/29 23:33:59 1.2 @@ -1,8 +1,15 @@ package org.smoby.graph; +import com.hp.hpl.jena.rdf.model.*; + /** * An object that represents the object of a mapping. */ -public interface MOBYObject extends MOBYMappingElement +public class MOBYObject extends MOBYMappingElement { -} \ No newline at end of file + public MOBYObject(Resource resource, MOBYFixedCollection statements, + MOBYCollection nestedElements, Model underlying) + { + super(resource, statements, nestedElements, underlying); + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYSubject.java 2004/07/29 23:33:59 1.2 @@ -1,6 +1,9 @@ package org.smoby.graph; -import java.net.URI; +import org.smoby.graph.*; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; /** * An object that represents the subject of one or more mappings. In @@ -16,11 +19,27 @@ * of which can itself be either a moby:Subject, an RDF data structure, * or both. This collection of elements is returned by getNestedMappings(). */ -public interface MOBYSubject extends MOBYMappingElement +public class MOBYSubject extends MOBYMappingElement { + /** + * The collection of direct mappings, i.e. moby:mapsTo statements + * whose subject is this. + */ + private MOBYUnorderedCollection directMappings; + + public MOBYSubject(Resource resource, MOBYFixedCollection statements, + MOBYUnorderedCollection directMappings, + MOBYCollection nestedMappings, Model underlying) + { + super(resource, statements, nestedMappings, underlying); + this.directMappings = directMappings; + } + /** * Return a resizable, unordered collection of the MOBYNode instances, * which are objects of mapsTo statements, whose subjects are this. */ - public MOBYUnorderedCollection getDirectMappings(); -} \ No newline at end of file + public MOBYUnorderedCollection getDirectMappings() { + return directMappings; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java 2004/05/24 22:05:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/MOBYPropertyValueException.java 2004/07/29 23:33:59 1.2 @@ -1,6 +1,5 @@ package org.smoby.graph; - public class MOBYPropertyValueException extends Exception { public MOBYPropertyValueException(String message) { From mwilkinson at pub.open-bio.org Thu Jul 29 23:34:06 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 19:34:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNY6mG020893@pub.open-bio.org> mwilkinson Thu Jul 29 19:34:06 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv20855/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: okay,now it works properly. A new parameter RDF is returned in the Registration XML. This holds the RDF signature of your service. moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 21:53:54 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 23:34:06 1.7 @@ -30,11 +30,11 @@ sub serialize { - my ($model) = @_; + my ($self) = @_; my $xml = ''; my $serializer = new RDF::Core::Model::Serializer( - Model=>$model, + Model=>$self->model, Output=>\$xml, getNamespaces => \&xmlNamespaces, # this only works with a patch!!!!!!!!!!!!!!!! ); From mwilkinson at pub.open-bio.org Thu Jul 29 23:34:06 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 19:34:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNY6n7020874@pub.open-bio.org> mwilkinson Thu Jul 29 19:34:06 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv20855/MOBY Modified Files: Central.pm Log Message: okay,now it works properly. A new parameter RDF is returned in the Registration XML. This holds the RDF signature of your service. moby-live/Perl/MOBY Central.pm,1.134,1.135 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.134 retrieving revision 1.135 diff -u -r1.134 -r1.135 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 21:53:53 1.134 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 23:34:06 1.135 @@ -1167,24 +1167,19 @@ # this is roundabout, I agree, but it is the most re-usable way to go at # the moment. - my ($si, $reg) = &findService(qw{ + my ($si, $reg) = &findService('',' $AuthURI; $serviceName; - "}); + '); unless ($si){ $SVC->DELETE_THYSELF; return &_error("Registration Failed - newly registered service could not be discovered",""); } - my $service = shift @{$si}; - unless ($service){ - $SVC->DELETE_THYSELF; - return &_error("Registration Failed - newly registered service could not be discovered",""); - } - - my $services = MOBY::Client::Central::_parseServices('', '', $service); + use MOBY::Client::Central; + my $services = MOBY::Client::Central::_parseServices('', '', $si); my $service_instance = shift @{$services}; my $storage = new RDF::Core::Storage::Memory; my $model = new RDF::Core::Model (Storage => $storage); @@ -1670,7 +1665,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if (scalar @{$findme{keywords}}){ + if ($findme{keywords} && (scalar @{$findme{keywords}})){ ++$criterion_count; $debug && _LOG("Keywords added; criterion count is now $criterion_count\n"); my $searchstring; @@ -1694,7 +1689,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if (scalar @{$findme{inputObjects}}){ + if ($findme{inputObjects} && (scalar @{$findme{inputObjects}})){ ++$criterion_count; $debug && _LOG("inputObject added; criterion count is now $criterion_count\n"); my $obj = (shift @{$findme{inputObjects}}); @@ -1727,7 +1722,7 @@ ++$valid_service_ids{$_}; } } - if (scalar @{$findme{outputObjects}}){ + if ($findme{outputObjects} && (scalar @{$findme{outputObjects}})){ ++$criterion_count; $debug && _LOG("outputObject added; criterion count is now $criterion_count\n"); my $obj = (shift @{$findme{outputObjects}}); From gss at pub.open-bio.org Thu Jul 29 23:34:44 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:34:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNYi6a020925@pub.open-bio.org> gss Thu Jul 29 19:34:43 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools In directory pub.open-bio.org:/tmp/cvs-serv20901/src/org/smoby/graph/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools added to the repository moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 23:34:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:34:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292334.i6TNYks3020959@pub.open-bio.org> gss Thu Jul 29 19:34:45 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools In directory pub.open-bio.org:/tmp/cvs-serv20938/src/org/smoby/graph/tools Added Files: MOBYProviderTraversalException.java MOBYProviderXMLGenerator.java MOBYProviderVisitor.java MOBYProviderTraverser.java Log Message: Visitor pattern for MOBY graphs, with example moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools MOBYProviderTraversalException.java,NONE,1.1 MOBYProviderXMLGenerator.java,NONE,1.1 MOBYProviderVisitor.java,NONE,1.1 MOBYProviderTraverser.java,NONE,1.1 From gss at pub.open-bio.org Thu Jul 29 23:35:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:35:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292335.i6TNZ9Ta020991@pub.open-bio.org> gss Thu Jul 29 19:35:09 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser In directory pub.open-bio.org:/tmp/cvs-serv20966/src/org/smoby/parser Modified Files: Parser.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/19 18:21:36 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/07/29 23:35:09 1.7 @@ -4,7 +4,6 @@ import java.net.*; import java.util.*; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.parser.*; import org.smoby.tools.ModelRetriever; import org.smoby.tools.Util; @@ -179,7 +178,7 @@ // Create and return an unordered collection of the parsed providers // - return MOBYObjectFactory.newUnorderedCollection(null, providers, null); + return new MOBYUnorderedCollection(null, providers, null); } /** @@ -211,9 +210,9 @@ // Create and return a new Provider object using the provider URI, name, // oneLineDescription, aboutURI, and collection of operatesOn subgraphs // - return MOBYObjectFactory.newProvider( + return new MOBYProvider( provider, name, oneLiner, aboutURI, - MOBYObjectFactory.newUnorderedCollection(provider, operatesOn, model), + new MOBYUnorderedCollection(provider, operatesOn, model), model); } @@ -234,7 +233,7 @@ // hasMapping property that leads to its mapping subgraph. // Resource hasMapping = getResourcePropertyValue(res, MOBY.hasMapping); - return MOBYObjectFactory.newGraph(res, parseHasMapping(hasMapping), model); + return new MOBYGraph(res, parseHasMapping(hasMapping), model); } else { @@ -318,9 +317,9 @@ // Create and return a Subject to describe this hasMapping subgraph // - return MOBYObjectFactory.newSubject(res, - MOBYObjectFactory.newFixedCollection(res, statements, model), - MOBYObjectFactory.newUnorderedCollection(res, directMappings, model), + return new MOBYSubject(res, + new MOBYFixedCollection(res, statements, model), + new MOBYUnorderedCollection(res, directMappings, model), collectionFor(res, nestedMappings), model); } @@ -362,8 +361,8 @@ // Create and return a new MOBYObject // Model model = res.getModel(); - return MOBYObjectFactory.newObject(res, - MOBYObjectFactory.newFixedCollection(res, statements, model), + return new MOBYObject(res, + new MOBYFixedCollection(res, statements, model), collectionFor(res, nested), model); } @@ -395,7 +394,7 @@ if (isMobyProperty(p, model)) { MOBYPropertyValueStatement pvalStmt = - MOBYObjectFactory.newPropertyValueStatement(stmt, model); + new MOBYPropertyValueStatement(stmt, model); Statement s = p.getProperty(RDFS.range); @@ -403,15 +402,15 @@ { Resource range = (Resource) s.getObject(); if (range.equals(XSD.date)) { - pvalStmt.setConstraint(MOBYObjectFactory.newDateConstraint()); + pvalStmt.setConstraint(new MOBYDateConstraint()); } else if (range.equals(XSD.integer)) { - pvalStmt.setConstraint(MOBYObjectFactory.newIntegerConstraint()); + pvalStmt.setConstraint(new MOBYIntegerConstraint()); } else if (range.equals(XSD.nonNegativeInteger)) { pvalStmt.setConstraint( - MOBYObjectFactory.newNonNegativeIntegerConstraint()); + new MOBYNonNegativeIntegerConstraint()); } else if (range.equals(XSD.nonPositiveInteger)) { pvalStmt.setConstraint( - MOBYObjectFactory.newNonPositiveIntegerConstraint()); + new MOBYNonPositiveIntegerConstraint()); } } @@ -486,13 +485,13 @@ private MOBYCollection collectionFor(Resource res, List elements) { if (isList(res)) { - return MOBYObjectFactory.newFixedCollection(res, elements, res.getModel()); + return new MOBYFixedCollection(res, elements, res.getModel()); } else if (isBag(res)) { - return MOBYObjectFactory.newUnorderedCollection(res, elements, res.getModel()); + return new MOBYUnorderedCollection(res, elements, res.getModel()); } else if (isSeq(res)) { - return MOBYObjectFactory.newOrderedCollection(res, elements, res.getModel()); + return new MOBYOrderedCollection(res, elements, res.getModel()); } else if (isAlt(res)) { - return MOBYObjectFactory.newEnumeration(res, elements, res.getModel()); + return new MOBYEnumeration(res, elements, res.getModel()); } else { return null; } From gss at pub.open-bio.org Thu Jul 29 23:37:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:37:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292337.i6TNbxZw021051@pub.open-bio.org> gss Thu Jul 29 19:37:59 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21026/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools DiscoveryQuery.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/15 20:27:13 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/29 23:37:59 1.2 @@ -8,7 +8,6 @@ import org.smoby.ref.tools.db.*; import org.smoby.tools.Util; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.vocabulary.*; import com.hp.hpl.jena.db.*; @@ -111,7 +110,7 @@ Model dbModel = null; try { - Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying(); + Model queryModel = ((MOBYProvider) queryProvider).getUnderlying(); String queryString = buildQueryString(queryModel); StorageManager manager = new StorageManager(); dbModel = manager.openDBModel(); @@ -129,7 +128,7 @@ } results.close(); - MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet(); + MOBYProviderSet returnSet = new MOBYProviderSet(); for (Iterator it = matching.iterator(); it.hasNext();) { From gss at pub.open-bio.org Thu Jul 29 23:38:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:38:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292338.i6TNce9x021089@pub.open-bio.org> gss Thu Jul 29 19:38:40 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example In directory pub.open-bio.org:/tmp/cvs-serv21064/src/org/smoby/ref/servlets/example Modified Files: HelloWorldServlet.java Log Message: Remove use of MOBYObjectFactory moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example HelloWorldServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/21 22:01:19 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/servlets/example/HelloWorldServlet.java 2004/07/29 23:38:40 1.3 @@ -6,7 +6,6 @@ import javax.servlet.http.*; import org.smoby.graph.*; -import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.ref.servlets.*; import org.smoby.servlet.*; @@ -34,7 +33,7 @@ MOBYGraph graph = (MOBYGraph) provider.getOperatesOn().iterator().next(); - MOBYSubject subject = (MOBYSubject) graph.gethasMapping(); + MOBYSubject subject = (MOBYSubject) graph.getHasMapping(); MOBYObject object = (MOBYObject) subject.getDirectMappings().iterator().next(); @@ -43,7 +42,7 @@ object.getPropertyValueStatements().iterator().next(); stmt.setPropertyValue( - MOBYObjectFactory.newLiteralValue("Hello, world!")); + new MOBYLiteral("Hello, world!")); } // Silently ignore graphs without the required form From gss at pub.open-bio.org Thu Jul 29 23:38:53 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:38:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292338.i6TNcr5E021119@pub.open-bio.org> gss Thu Jul 29 19:38:53 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21094/src/org/smoby/ref/tools Modified Files: KeywordFinder.java Log Message: Remove use of MOBYObjectFactory moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools KeywordFinder.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java 2004/07/21 22:01:19 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/KeywordFinder.java 2004/07/29 23:38:53 1.2 @@ -85,7 +85,7 @@ if (node instanceof MOBYGraph) { MOBYGraph graph = (MOBYGraph) node; - addSubjectKeywordsFor(graph.gethasMapping()); + addSubjectKeywordsFor(graph.getHasMapping()); } else if (node instanceof MOBYCollection) { From gss at pub.open-bio.org Thu Jul 29 23:39:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:39:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292339.i6TNdH12021149@pub.open-bio.org> gss Thu Jul 29 19:39:17 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv21124/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Use new graph structure moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageManager.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/21 22:01:20 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/29 23:39:17 1.3 @@ -1,7 +1,6 @@ package org.smoby.ref.tools.db; import org.smoby.graph.*; -import org.smoby.graph.impl.*; import org.smoby.ref.tools.*; import org.smoby.tools.Util; import org.smoby.vocabulary.*; @@ -60,7 +59,7 @@ public void registerProvider(MOBYProvider provider, Date lastModifiedDate) throws StorageException { - Model model = ((MOBYProviderImpl) provider).getUnderlying(); + Model model = ((MOBYProvider) provider).getUnderlying(); Model dbModel = null; String uriString = provider.getResource().getURI(); Resource uri = model.createResource(uriString); From gss at pub.open-bio.org Thu Jul 29 23:44:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNiaFR021283@pub.open-bio.org> gss Thu Jul 29 19:44:36 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc In directory pub.open-bio.org:/tmp/cvs-serv21259/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc added to the repository moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/developer/doc/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Jul 29 23:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicbn021313@pub.open-bio.org> gss Thu Jul 29 19:44:37 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/15 20:30:18 1.11 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/07/29 23:44:37 1.12 @@ -6,7 +6,6 @@ import javax.servlet.http.*; import org.smoby.servlet.*; import org.smoby.graph.*; -import org.smoby.graph.impl.MOBYObjectFactory; import org.smoby.vocabulary.*; import com.acmepubs.vocabulary.*; @@ -54,7 +53,7 @@ // The subject of the graph should be a MOBYSubject // - MOBYSubject subject = (MOBYSubject) graph.gethasMapping(); + MOBYSubject subject = (MOBYSubject) graph.getHasMapping(); // That object should have a single subproperty of moby:Property, // namely geneSymbol; its value should be a literal @@ -77,8 +76,7 @@ // based on a base URI string and the geneSymbol that was passed // String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus="; - literal = MOBYObjectFactory.newLiteralValue( - baseURI + geneSymbol); + literal = new MOBYLiteral(baseURI + geneSymbol); stmt.setPropertyValue(literal); } } From gss at pub.open-bio.org Thu Jul 29 23:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNic60021333@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/server/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/06/18 21:42:34 1.6 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/07/29 23:44:38 1.7 @@ -111,7 +111,7 @@ Model dbModel = null; try { - Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying(); + Model queryModel = queryProvider.getUnderlying(); String queryString = buildQueryString(queryModel); StorageManager manager = new StorageManager(); dbModel = manager.openDBModel(); @@ -129,7 +129,7 @@ } results.close(); - MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet(); + MOBYProviderSet returnSet = new MOBYProviderSet(); for (Iterator it = matching.iterator(); it.hasNext();) { From gss at pub.open-bio.org Thu Jul 29 23:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicgw021373@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/06/18 21:42:34 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/07/29 23:44:38 1.6 @@ -58,7 +58,7 @@ public void registerProvider(MOBYProvider provider, Date lastModifiedDate) throws StorageException { - Model model = ((MOBYProviderImpl) provider).getUnderlying(); + Model model = provider.getUnderlying(); Model dbModel = null; String uriString = provider.getURI(); Resource uri = model.createResource(uriString); From gss at pub.open-bio.org Thu Jul 29 23:44:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 29 Jul 2004 19:44:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407292344.i6TNicra021352@pub.open-bio.org> gss Thu Jul 29 19:44:38 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients In directory pub.open-bio.org:/tmp/cvs-serv21288/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients Modified Files: SimpleProviderEngagerPanel.java Log Message: Minor changes moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/15 20:20:37 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/SimpleProviderEngagerPanel.java 2004/07/29 23:44:38 1.3 @@ -120,7 +120,7 @@ } else { - String graphURI = provider.getURI(); + String graphURI = provider.getResource().getURI(); HTTPRequest request = HTTPRequest.newPostRequest(graphURI); request.addParameter("graph", graphString); HTTPResponse response = request.send(); From mwilkinson at pub.open-bio.org Fri Jul 30 00:07:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:07:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300007.i6U07IUv021549@pub.open-bio.org> mwilkinson Thu Jul 29 20:07:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv21507/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: the adaptor now writes to a new field in the database - signatureURL - which is where Nina's agent expects to find the RDF corresponding to the service. This can be null, if you want to temporarily register a service. moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/26 17:09:09 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:07:18 1.4 @@ -204,7 +204,7 @@ my ($self, %args) = @_; my $dbh = $self->dbh; - $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description) values (?,?,?,?,?,?,?,?)}, + $dbh->do(q{insert into service_instance (category, servicename, service_type_uri, authority_id, url, contact_email, authoritative, description, signatureURL) values (?,?,?,?,?,?,?,?,?)}, undef, $args{'category'}, $args{'servicename'}, @@ -213,7 +213,8 @@ $args{'url'}, $args{'contact_email'}, $args{'authoritative'}, - $args{'description'}); + $args{'description'}, + $args{'signatureURL'}); my $id = $dbh->{mysql_insertid}; return $id; From mwilkinson at pub.open-bio.org Fri Jul 30 00:07:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:07:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300007.i6U07IXA021530@pub.open-bio.org> mwilkinson Thu Jul 29 20:07:18 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv21507/MOBY Modified Files: Central.pm service_instance.pm Log Message: the adaptor now writes to a new field in the database - signatureURL - which is where Nina's agent expects to find the RDF corresponding to the service. This can be null, if you want to temporarily register a service. moby-live/Perl/MOBY Central.pm,1.135,1.136 service_instance.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.135 retrieving revision 1.136 diff -u -r1.135 -r1.136 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/29 23:34:06 1.135 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:07:18 1.136 @@ -1082,11 +1082,12 @@ sub registerService { my ($pkg, $payload) = @_; - my ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARY) = &_registerServicePayload($payload); + my ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARY, $signatureURL) = &_registerServicePayload($payload); $authoritativeService = defined($authoritativeService)?1:0; my $error; $error .="missing serviceName \n" unless defined $serviceName; $error .="missing serviceType \n" unless defined $serviceType; + $error .="missing signatureURL \n" unless defined $signatureURL; $error .="missing authURI \n" unless defined $AuthURI; $error .="missing contactEmail \n" unless defined $contactEmail; return &_error("Malformed authURI - must not have an http:// prefix","") if $AuthURI =~ '[/:]'; @@ -1141,6 +1142,7 @@ contact_email => $contactEmail, authoritative => $authoritativeService, description => $desc, + signatureURL => $signatureURL, ); return &_error("Service registration failed for unknown reasons","") if (!defined $SVC); @@ -1167,13 +1169,10 @@ # this is roundabout, I agree, but it is the most re-usable way to go at # the moment. - my ($si, $reg) = &findService('',' - - + my ($si, $reg) = &findService(''," $AuthURI; $serviceName; - - '); + "); unless ($si){ $SVC->DELETE_THYSELF; return &_error("Registration Failed - newly registered service could not be discovered",""); @@ -1356,13 +1355,15 @@ my $contactEmail = &_nodeTextContent($Object, "contactEmail"); my $authoritativeService = &_nodeTextContent($Object, "authoritativeService"); my $URL = &_nodeTextContent($Object, "URL"); + my $signatureURL = &_nodeTextContent($Object, "signatureURL"); my $desc = &_nodeTextContent($Object, "Description"); my $INPUTS = &_nodeRawContent($Object, "Input"); # returns array ref my $OUTPUTS = &_nodeRawContent($Object, "Output"); # returns array ref my $SECONDARIES = &_nodeRawContent($Object, "secondaryArticles"); # returns array ref - return ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARIES); + return ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $authoritativeService, $desc, $Category, $INPUTS, $OUTPUTS, $SECONDARIES, $signatureURL); } + sub _extractObjectTypes { my ($DOM) = @_; # DOM is either a or a article $debug && &_LOG("\n\n\nExtracting object types from \n$DOM \n\n"); @@ -2878,7 +2879,7 @@ my $output=""; my $sth = $dbh->prepare(q{ select - category, url, servicename, service_type_uri, authority_id, description, authoritative, contact_email + category, url, servicename, service_type_uri, authority_id, description, authoritative, contact_email, signatureURL from service_instance where service_instance_id = ?}); my $sth_simple_in = $dbh->prepare("select object_type_uri, namespace_type_uris, article_name from simple_input where service_instance_id=? and collection_input_id IS NULL"); @@ -2896,8 +2897,9 @@ foreach (@ids){ $sth->execute($_); - my ($category, $url, $servicename, $service_type_uri, $authority_id, $desc, $authoritative, $email) = $sth->fetchrow_array; + my ($category, $url, $servicename, $service_type_uri, $authority_id, $desc, $authoritative, $email, $signatureURL) = $sth->fetchrow_array; #print "\n\nAFTER EXECUTE $category, $servicename, $service_type_uri, $authority_id, $desc, $authoritative\n\n"; + $signatureURL ||=""; next unless ($servicename && $authority_id); my $service_type = $OSserv->getServiceCommonName($service_type_uri); my ($authURI) = $dbh->selectrow_array(q{select authority_uri from authority where authority_id=?},undef,$authority_id); @@ -2907,6 +2909,7 @@ $output .= "\t$category\n"; $output .= "\t\n$desc\n\t\n"; $output .= "\t$email\n"; + $output .= "\t$signatureURL\n"; $output .= "\t$url\n"; $output .="\t\n"; $sth_simple_in->execute($_); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/09 00:21:53 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:07:18 1.7 @@ -66,6 +66,7 @@ service_type_uri => [undef, 'read/write'], authority => [undef, 'read/write'], authority_uri => [undef, 'read/write'], + signatureURL => [undef, 'read/write'], url => [undef, 'read/write'], inputs => [undef, 'read/write'], outputs => [undef, 'read/write'], @@ -128,6 +129,12 @@ (defined $val) && ($self->{url} = $val); return $self->{url} } + sub signatureURL{ + my ($self, $val) = @_; + if (defined $val && $self->signatureURL){return undef} + (defined $val) && ($self->{signatureURL} = $val); + return $self->{signatureURL} + } sub contact_email { my ($self, $val) = @_; if (defined $val && $self->contact_email){return undef} @@ -240,7 +247,10 @@ url => $self->url, contact_email => $self->contact_email, authoritative => $self->authoritative, - description => $self->description); + description => $self->description, + signatureURL => $self->signatureURL, + ); + $self->service_instance_id($id); $self->{__exists__} = 1; # this service now exists } else { # if it doesn't exist, and you havne't given me anyting I need to create it, then bail out From mwilkinson at pub.open-bio.org Fri Jul 30 00:14:15 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:14:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300014.i6U0EFkP021656@pub.open-bio.org> mwilkinson Thu Jul 29 20:14:15 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv21637/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: adding the new parameter into the test suite moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.19,1.20 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/12 00:39:37 1.19 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:14:15 1.20 @@ -159,6 +159,7 @@ serviceName => "myfirstservice", serviceType => "Retrieval", authURI => "www.illuminae.com", + signatureURL => "http://www.illuminae.com/somewhere", contactEmail => 'your at mail.address', description => "this is my first service", category => "moby", @@ -182,6 +183,7 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your at mail.address', + signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -198,6 +200,7 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your at mail.address', + signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", From mwilkinson at pub.open-bio.org Fri Jul 30 00:16:32 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:16:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300016.i6U0GWli021724@pub.open-bio.org> mwilkinson Thu Jul 29 20:16:32 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv21705/MOBY/Client Modified Files: Central.pm Log Message: adding the new parameter into the client library moby-live/Perl/MOBY/Client Central.pm,1.77,1.78 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.77 retrieving revision 1.78 diff -u -r1.77 -r1.78 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/29 21:53:54 1.77 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/30 00:16:32 1.78 @@ -706,6 +706,7 @@ my $email = $a{contactEmail}; $email ||=""; my $URL = $a{URL}; $URL ||=""; my $desc = $a{description}; $desc ||=""; + my $signatureURL = $a{signatureURL}; $signatureURL ||=""; my $Category = lc($a{category}); chomp $Category; $Category ||=""; return $self->errorRegXML("Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category") unless (($Category eq 'moby') || ($Category eq 'wsdl')); return $self->errorRegXML("All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary") unless ( @@ -717,6 +718,7 @@ $name $type + $signatureURL $URL $authURI $email"; From mwilkinson at pub.open-bio.org Fri Jul 30 00:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:40:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9Vi021885@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv21862/MOBY Modified Files: Central.pm service_instance.pm Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/MOBY Central.pm,1.136,1.137 service_instance.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.136 retrieving revision 1.137 diff -u -r1.136 -r1.137 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:07:18 1.136 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:40:09 1.137 @@ -1087,7 +1087,7 @@ my $error; $error .="missing serviceName \n" unless defined $serviceName; $error .="missing serviceType \n" unless defined $serviceType; - $error .="missing signatureURL \n" unless defined $signatureURL; +# $error .="missing signatureURL \n" unless defined $signatureURL; $error .="missing authURI \n" unless defined $AuthURI; $error .="missing contactEmail \n" unless defined $contactEmail; return &_error("Malformed authURI - must not have an http:// prefix","") if $AuthURI =~ '[/:]'; @@ -1431,9 +1431,12 @@ return &_error("The service specified by authority=$authURI servicename=$serviceName does not exist in the registry", "") unless (MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI, test => 1)); my $SERVICE = MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI); - my $result = $SERVICE->DELETE_THYSELF; - - if ($result){ + if ($SERVICE->signatureURL){ + return &_error("it is illegal to register a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); + } + + my $result = $SERVICE->DELETE_THYSELF; + if ($result){ return &_success("Service Deregistered Successfully",""); } else { return &_error("Service deletion failed for unknown reasons",""); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:07:18 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2004/07/30 00:40:09 1.8 @@ -231,6 +231,8 @@ $self->contact_email($existing_service->{'email'}); $self->description($existing_service->{'desc'}); $self->authority($existing_service->{'authURI'}); + $self->signatureURL($existing_service->{'signatureURL'}); + $self->{__exists__} = 1; # this service already existed } elsif (!($existing_service) # if it doesn't exist && (defined $self->category) # and you have given me things I need to create it From mwilkinson at pub.open-bio.org Fri Jul 30 00:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:40:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9gp021924@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv21862/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.20,1.21 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:14:15 1.20 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:40:09 1.21 @@ -1,7 +1,7 @@ #!/usr/bin/perl -w use MOBY::Client::Central; -my $v = 1 if ($ARGV[0] eq "verbose"); +my $v = 1 if ($ARGV[0] && ($ARGV[0] eq "verbose")); sub TEST { # test of Registration object ($reg, $test, $expect) = @_; From mwilkinson at pub.open-bio.org Fri Jul 30 00:40:09 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 20:40:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300040.i6U0e9qT021904@pub.open-bio.org> mwilkinson Thu Jul 29 20:40:09 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv21862/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: deprecating the deregisterService routine... kinda... it still works, but only if the service was registered without a signatureURL moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:07:18 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:40:09 1.5 @@ -169,7 +169,7 @@ my ($self, %args) = @_; my $dbh = $self->dbh; - my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist? + my ($serviceid, $category, $name, $typeURI, $authURI,$url,$email,$authoritative,$desc, $signatureURL) = $dbh->selectrow_array( # does this service already exist? q{select service_instance_id, category, @@ -179,7 +179,8 @@ url, service_instance.contact_email, authoritative, - description + description, + signatureURL from service_instance, authority where service_instance.authority_id = authority.authority_id From mwilkinson at pub.open-bio.org Fri Jul 30 01:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 21:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1EiwK022137@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory pub.open-bio.org:/tmp/cvs-serv22099/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 00:40:09 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2004/07/30 01:14:44 1.6 @@ -193,6 +193,7 @@ name => $name, servcetype => $typeURI, authURI => $authURI, + signatureURL => $signatureURL, url => $url, email => $email, authoritative => $authoritative, From mwilkinson at pub.open-bio.org Fri Jul 30 01:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 21:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1Eium022118@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv22099/MOBY Modified Files: Central.pm Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/MOBY Central.pm,1.137,1.138 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.137 retrieving revision 1.138 diff -u -r1.137 -r1.138 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 00:40:09 1.137 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 01:14:44 1.138 @@ -1432,7 +1432,7 @@ return &_error("The service specified by authority=$authURI servicename=$serviceName does not exist in the registry", "") unless (MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI, test => 1)); my $SERVICE = MOBY::service_instance->new(servicename => $serviceName, authority_uri => $authURI); if ($SERVICE->signatureURL){ - return &_error("it is illegal to register a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); + return &_error("it is illegal to deregister a service that has a signatureURL. Such services must be deregistered by deleting the RDF at the location identified by the signatureURL",""); } my $result = $SERVICE->DELETE_THYSELF; From mwilkinson at pub.open-bio.org Fri Jul 30 01:14:44 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 29 Jul 2004 21:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200407300114.i6U1EixZ022157@pub.open-bio.org> mwilkinson Thu Jul 29 21:14:44 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv22099/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: last tweaks to provide protection to services that have a signatureURL. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.21,1.22 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 00:40:09 1.21 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 01:14:44 1.22 @@ -159,7 +159,6 @@ serviceName => "myfirstservice", serviceType => "Retrieval", authURI => "www.illuminae.com", - signatureURL => "http://www.illuminae.com/somewhere", contactEmail => 'your at mail.address', description => "this is my first service", category => "moby", @@ -183,7 +182,6 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your at mail.address', - signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -200,7 +198,6 @@ serviceType => "Retrieval", authURI => "www.illuminae.com", contactEmail => 'your at mail.address', - signatureURL => "http://www.illuminae.com/somewhere", description => "this is my first service", category => "moby", URL => "http://illuminae/cgi-bin/service.pl", @@ -266,10 +263,14 @@ serviceName => "myfirstservice", authURI => "www.illuminae.com", ), 28, 1); - -TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 28, 1); -TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 29, 1); -TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 30, 1); +#TEST($C->deregisterService( +# serviceName => "getDragonSimpleAnnotatedImages", +# authURI => "www.illuminae.com", +# ), 29, 0); # cant deregister a service with a signatureURL + +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject2"), 30, 1); +TEST($C->deregisterObjectClass(objectType => "HypotheticalObject1"), 31, 1); +TEST($C->deregisterNamespace(namespaceType =>'HypotheticalNamespace1'), 32, 1); exit 0;